Flagging In Trees – What Causes Tree Branch Flagging

By: Teo Spengler

Tree branch flagging is not a pretty sight. What is branch flagging? It’s a condition when tree branches scattered throughout the tree’s crown turn brown and die. Various pests can cause flagging. If you want more information about tree branch flagging, including different causes of flagging damage to trees, read on.

What is Branch Flagging?

The condition called tree branch flagging occurs when a tree’s branches turn brown, wilt, or die. Usually, the branches are not all grouped together. Rather, you may see them scattered around the tree’s crown.

Flagging in trees can be due to cicada insects. The females use a sharp appendage on their abdomens to break open the bark of small, new tree branches to deposit eggs. The damaged young branches can then break off in the wind and fall to the ground. Although cicada-caused flagging in trees can drop large amounts of tree litter in your backyard, the tree branch flagging won’t kill vigorous specimens. Healthy branches will recover and keep on growing.

If you want to treat cicada-caused flagging damage to trees, prune out the affected branches. Do this when the tree is dormant and burn the detritus.

Flagging Damage to Trees from Other Causes

Cicadas are not the only causes of tree branch flagging. Flagging in trees, like oaks, can also result from Kermes scales, sap-feeding insects that damage many kinds of oak. Tan or brown, these scale bugs look like small globes attached to twigs. Treat with appropriate insecticides.

Flagging damage to trees can also be caused by twig girdlers and twig pruners. These are both types of beetle that attack oak, hickory, and other hardwood trees. You can limit flagging damage to trees from these beetles by raking up all fallen twigs and branches and burning them.

Another cause of flagging in trees is botryosphaeria canker, caused by a fungus. Botryosphaeria canker generally affects oak twigs, bending the leaves inward toward the twig. Usually, the leaves stay on the twig but they turn brown. This cause of flagging in trees is not serious and requires no treatment.

Thousand cankers disease is another invasive pest that damages black walnut. This is a more serious condition and may require special treatment. Take a sample of the flagging to your garden store and ask them for suggestions.

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Read more about General Tree Care

Pine Tree Flag

The Tree Flag (or the Appeal to Heaven Flag) was one of the flags which was used during the American Revolution. The flag, which featured a pine tree with the motto "An Appeal to Heaven," or less frequently "An Appeal to God", was originally used by a squadron of six cruisers which were commissioned under George Washington's authority as commander in chief of the Continental Army in October 1775. It was also used by Massachusetts state navy vessels in addition to privateers sailing from Massachusetts. [1]

How to Prune Ponderosa Pine Trees

Ponderosa pine trees (Pinus ponderosa) are stately trees that prefer locations on the edge of forests and wide-open spaces. They do well in cooler, moister conditions, growing among western larch, Douglas fir, lodgepole pine and quaking aspen. The hardy tree also tolerates drought. Ponderosa pines grow needles that are bundled in groups of three and long pine cones. The needles are 5 to 10 inches in length, whereas the pine cones are 3 to 6 inches long. Mature trees can achieve heights of 180 feet. Prune Ponderosa pines to keep them healthy and improve their appearance.

  • Ponderosa pine trees (Pinus ponderosa) are stately trees that prefer locations on the edge of forests and wide-open spaces.

Prune Ponderosa pine trees in the late fall or winter time, when the growth period has slowed down. Pruning during the spring or summer may damage the tree and invite diplodia, a conifer disease, to infect the tree.

Climb the ladder to get a full look at the shape of the Ponderosa pine tree. Look for dead, diseased or damaged branches.

Cut off dead wood with shears or a pruning saw, depending on the thickness of the branches. This will not affect the tree's photosynthesis process.

Place all cuts just outside the collar, which is the swollen section at the base of the unwanted branches. The tree will heal faster and you will minimize the risk of pest or disease infestation.

  • Prune Ponderosa pine trees in the late fall or winter time, when the growth period has slowed down.
  • Cut off dead wood with shears or a pruning saw, depending on the thickness of the branches.

Remove crossing branches, along with those that rub up against each other. The goal is to open up the tree's canopy to allow sunlight and air circulation. These branches are blocking the nutrients from getting to other parts of the Ponderosa pine tree.

Trim off shoots that are growing along the tree trunk. Pinch back the ends of new growth by hand to promote the tree to grow in a bushier fashion.

Wear gloves to protect your hands.

Wear eye protection when using a saw of any kind.

Don't attempt to prune very large and tall Ponderosa pine trees alone. Get a professional tree company to tackle the project.

How to Manage Pests

Phytophthora Root and Crown Rot in the Garden

General aboveground symptoms of tree with crown and root disease.

Purpling and reddening of older leaves is a symptom of Phytophthora root rot.

Darkened bark and wood tissue is a symptom of Phytophthora crown and root rot.

Reddish brown Phytophthora crown rot canker with zonate margin.

Stunting and discoloration from Phytophthora root rot on pepper roots.

Several species of soilborne pathogens in the genus Phytophthora cause crown and root rot diseases of herbaceous and woody plants. Almost all fruit and nut trees, as well as most ornamental trees and shrubs (including many California natives), can develop Phytophthora rot if soil around the base of the plant remains wet for prolonged periods, or when planted too deeply. Tomatoes, peppers, eggplant, and other vegetable crops can also be affected by Phytophthora rot. In trees and shrubs, the pathogen kills plants by growing from the roots up through the root crown and into the lower trunk, where it kills the inner bark and causes a browning of the outer layer of sapwood. In many of these crops, different species of Phytophthora are involved. Losses to Phytophthora are minimized by providing good soil drainage and selecting the most tolerant rootstocks or varieties available. In general, Phytophthora requires warm, moist soils in order to cause disease. Another species of Phytophthora, Phytophthora ramorum, causes sudden oak death, which has very different symptoms and management than the species discussed here. See Pest Note: Sudden Oak Death in California.


The leaves of plants affected by Phytophthora rot appear drought stressed. Trees or plants often wilt and die rapidly with the first warm weather of the season. Leaves may turn dull green, yellow, or in some cases red or purplish. Often, only plants in the most poorly drained area of the field or garden are affected. Phytophthora infections typically kill young trees, because their root systems and crown areas are small compared to those of mature trees.

Symptoms may develop first on one branch or stem then spread to the rest of a tree or plant. Trees may decline over a period of years before finally dying or they may be killed in a single season. Slow decline occurs when the roots are attacked rapid decline occurs when the crown or basal stem is attacked and girdled, the damage completely encircling the stem in a single season.

Symptoms on roots and crowns may vary somewhat depending on the species of Phytophthora involved, the plant being attacked, the resistance of the plant variety, and soil moisture and temperature. In general, trees affected by Phytophthora develop darkened areas in the bark around the crown and upper roots. Gum or dark sap may ooze from the margins of the diseased trunk area. If bark tissue is carefully cut away, reddish brown streaks or zones can be seen in the inner bark and outer layer of wood. No mycelium (slender filaments of a fungus body) is visible in between the bark and wood in trees affected by Phytophthora, distinguishing this disease from Armillaria root rot, which is caused by a true fungus.

When tomatoes and eggplants are affected by Phytophthora root rot, roots of all sizes develop water-soaked spots that dry out and turn a chocolate brown as the disease becomes advanced. Early infections, caused by Phytophthora and other pathogens that cause damping-off diseases, kill seedlings. For more information on damping-off diseases, see Pest Notes: Damping-Off Diseases in the Garden. Later infections reduce plant vigor and may cause collapse and death of the plant. If you cut infected tap roots in cross section, you will see that the stele (central core of conducting tissue) is brownish above the rot lesions. Stele discoloration may extend into the lower stem.


Phytophthora species are soil-inhabiting pathogens that are favored by wet conditions. Although previously considered fungi, Phytophthora species are now considered to be in a separate classification called oomycetes. Species of Phytophthora produce resting spores that survive for years in moist soil in the absence of a suitable host. However, if the soil is completely dried out, these spores are less likely to survive for more than a few months. When a host is nearby and free water (water in soil pore spaces) is present in the soil, resting spores germinate to produce motile spores that can directly penetrate roots, branches, or crowns as long as free water is present. Wounds are not required for infection. Resting spores, decaying host tissue in the soil, and active cankers (disease-infected dead, sunken lesions in plant parts) can all be sources for new infections. The pathogen can be spread in splashing rain or irrigation water, in surface irrigation, and runoff water, and by movement of contaminated soil, equipment, or plant parts. Flooded and saturated soil favors the spread of Phytophthora to healthy plants.

Some Phytophthora species are favored by warm weather, some by cool weather. Root rots of avocado, citrus, and tomato are favored by warm conditions, developing most extensively in late spring and early summer. Decay of crown, trunk, and branches of other tree species are favored by cool, wet conditions. These decays develop most rapidly in late fall and early spring.


The most important factor in reducing the threat of Phytophthora rot is good water management. Avoid prolonged saturation of the soil or standing water around the base of trees or other susceptible plants. Irrigate only as much and as often as necessary in an orchard, keep track of the soil moisture around each tree and water only when necessary. If you irrigate trees with sprinklers, use low-angle sprinkler heads and splitters to avoid wetting the trunk and lower branches. If using a drip system, place the emitters at least a foot away from the trunk. Avoid planting susceptible species on poorly drained or shallow soils. Water stress and/or salinity make some plant species more susceptible to infection when wetted subsequently by irrigation or rains.

For all vegetable and orchard plants, provide good soil drainage. Good soil drainage is best provided before planting. Drainage should be plentiful to the rooting depth of the plants, generally 3 to 6 feet for trees, 2 to 4 feet for shrubs, and 1 to 2 feet for bedding plants. During favorable weather you do not want the roots and crown of a plant to remain wet for the 4 to 8 hours that are required for Phytophthora to infect the plant.

Provide adequate drainage by breaking through soil compaction and hardpan. In poorly drained soils, or in an area where you know Phytophthora is present, consider planting trees and shrubs on mounds. The mounds should be 8 to 10 inches high. Planting depth after settling should be no deeper than as received from the nursery, with the upper roots near the soil level and the graft union well above the soil line. Do not install irrigated turf around the base of trees, remove all weeds, and do not water the crown area directly. Never cover the graft union with soil or mulch. If you are not sure where the graft union is, ask someone at the nursery to show you and mark it. Raised beds provide good drainage in vegetable garden situations also. Group plants according to their irrigation needs. Separate those needing frequent, light irrigations, such as potatoes and strawberries, from those needing infrequent, deep irrigations, such as tomatoes and melons.

At the first signs of aboveground symptoms, examine the tree at the soil line for crown rot. Carefully cut away bark that looks affected. If crown rot is present, trees can sometimes be saved by removing soil from the base of the tree down to the top of the main roots and allowing the crown tissue to dry out.


It may be possible to slow the spread of Phytophthora within an orchard by avoiding movement of infested soil, water, and plant parts from an area where Phytophthora rot has developed. Surface and subsurface drainage water and anything that can move moist soil can carry the pathogen to a new area, including boots, car tires, and tools. If the physical setting allows drainage water to flow from infested to uninfected areas within the garden during wet weather, consider putting in drains to channel the water away from healthy plants.

Selection of planting stock

Plant only certified nursery stock from a reputable source, and choose the most resistant rootstocks or varieties available for your area. Less susceptible rootstocks or varieties are available for almonds and stone fruit, apples, cauliflower, and strawberries. Carefully select individual plants that are free of symptoms and/or that come from healthy lots of material.


If tomatoes have been affected by Phytophthora root rot, avoid planting tomatoes or other susceptible plants such as eggplant or peppers in the same soil for at least one or two seasons. Plant a resistant crop such as corn instead, or leave the soil unplanted and do not irrigate, but keep it well worked to allow the soil to dry as deeply as possible. Different species of Phytophthora attack beans and cole crops, so these plants can be substituted as well. Consult a nursery or farm advisor for possible alternatives in your area.

Chemical control

The most effective way of preventing Phytophthora rot diseases is to provide good drainage and to practice good water management. Along with the appropriate cultural controls, the fungicide fosetyl-al (Aliette) may be used on a number of ornamental plant species to help prevent Phytophthora infections. When applied as a foliar spray it is absorbed by foliage and moves into roots. However, do not rely on fungicide applications alone to control root and crown rot diseases.


Pest Notes: Damping-Off Diseases in the Garden. Aug. 2006. Perry, E. J. Oakland: Univ. Calif. Div. Agric. Nat. Res. Publ. 74132.

Pests of Landscape Trees and Shrubs. 2004. Dreistadt, S. H. Oakland: Univ. Calif. Div. Agric. Nat. Res. Publ. 3359.


Pest Notes: Phytophthora Root and Crown Rot in the Garden
UC ANR Publication 74133

Author: E. J. Perry, UC Cooperative Extension, Stanislaus County
Produced by IPM Education and Publications, University of California Statewide IPM Program

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Statewide IPM Program, Agriculture and Natural Resources, University of California
All contents copyright © 2019 The Regents of the University of California. All rights reserved.

For noncommercial purposes only, any Web site may link directly to this page. FOR ALL OTHER USES or more information, read Legal Notices. Unfortunately, we cannot provide individual solutions to specific pest problems. See our Home page, or in the U.S., contact your local Cooperative Extension office for assistance.

Agriculture and Natural Resources, University of California

How do I fix these problems?

  • Flagging- since this occurs naturally you don’t have to worry too much about it. It may help to water your Blue Atlas Cedar more often. You can also prune off the flagging areas and it won’t harm the tree.
  • Spider mites- to see if your Blue Atlas Cedar might have spider mites, take a white piece of paper and place it below a branch where green foliage meets brown foliage. Tap the branch above the paper. If you see tiny red/orange dots crawling on the paper, those are spider mites. One way to make spider mites go away is by using a strong spray of water all over the tree to get them off the tree. If the water isn’t working, you can use a neem oil spray or you could think of adding in beneficial insects such as lady bugs or lace wing flies that will go after the spider mites.
  • Weevils- to check for Weevils or other borers, look at the trunk and branches of the tree to see if there are any pin sized holes (the holes may also be oozing a sap-like substance). You can use a neem oil spray to combat them.
  • Sapsuckers- the holes that sapsuckers make will look very similar to weevil holes but sometimes they are bigger. You can keep sapsuckers at bay by placing reflective items by the tree, such as pinwheels, to scare them away.
  • Root rot- one way to check to see if your tree has root rot is to pull upward on the tree to see if it starts to pull out of the ground easily. If it does and the root ball is mostly gone, your Blue Atlas Cedar may be suffering from root rot and means the roots may not be functioning anymore. Sometimes it is possible to save the tree from root rot by changing the soil around the tree so it has better drainage and applying a fertilizer. In many cases though, you will have to remove the tree.
  • Fungus/bacteria- to see if your Blue Atlas Cedar may have cankers, look for a discolored indent in the bark of the tree. If cankers are left unattended, they can swell and girdle branches and the trunk. You can remove cankers by pruning them off during cold weather. If your tree is suffering from blight (caused by fungi), make sure you’re cleaning your pruning tools before moving on to other plants to prevent the spread of the fungi. You’ll want to prune and discard the infected parts of the tree including any branches that may have fallen to the ground. Because this fungi is usually spread through water and often times in wetter than normal Springs, make sure that the Blue Atlas Cedar is located in well-drained soils and doesn’t have standing water around it.
  • Over watering- this can be a cause of root rot. If you’re noticing that the area around your tree is overly wet on a continuous basis, try scaling back the amount of water you are giving by either dialing back on how often you water and/or the duration of watering.
  • Under watering- Blue Atlas Cedars have fairly shallow roots so they need to be watered often in the first couple of years that they’ve been planted. If the soil is sandy or drains really quickly or if it’s been excessively hot out, you should check the soil around your tree to see if it’s getting enough water. The soil should be wet about 1 inch below the surface. To fix this issue, simply water your Blue Atlas Cedar more often and/or for longer periods of time. Once established, Blue Atlas Cedars can tolerate mild periods of drought.
  • It may also help to talk with your lawn/landscape maintenance company about what fertilizers or other treatments are being placed near the tree to see if there might be other reasons your Blue Atlas Cedar is browning.

What are your tried and true ways of keeping your Blue Atlas Cedar looking beautiful and blue?

Time of year (when to prune)

The best time to prune live branches may depend on the desired results. Growth is maximized and defects are easier to see on deciduous trees if live-branch pruning is done just before growth resumes in early spring. Pruning when trees are dormant can minimize the risk of pest problems associated with wounding and allows trees to take advantage of the full growing season to begin closing and compartmentalizing wounds. A few tree pathogens, such as the oak wilt fungus, may be spread if pruning wounds are made when the pathogen vectors are active. Susceptible trees should not be pruned during active transmission periods. Trees with Dutch elm disease should have symptomatic branches removed as soon as a branch shows flagging. Susceptible, uninfected elms should not be pruned during the growing season in regions where this disease is a problem.

Removal of dying, diseased, broken, or dead limbs can be accomplished at any time with little negative effect on the tree. Plant growth can be reduced if live-branch pruning takes place during or soon after the initial growth flush. This is when trees have just expended a great deal of stored energy to produce roots, foliage, and early shoot growth so pruning at this time is usually not recommended due to the potential stresses. Stressed trees should not be pruned at this time.

Flowering can be prevented or enhanced by pruning at the appropriate time of the year. To retain the most flowers on landscape trees that bloom on current season’s growth, such as crape-myrtle (Lagerstroemia spp.) or linden (Tilia spp.), these trees are pruned in winter, prior to leaf emergence, or in the summer just after bloom. Plants that bloom on last season’s wood, such as Prunus, should be pruned just after bloom in order to preserve the flower display. Fruit trees can be pruned during the dormant season to enhance structure and distribute fruiting wood, and they are pruned after bloom to thin fruit.

Certain species of trees, such as maples (Acer spp.) and birches (Betula spp.), drip sap when pruned in the early spring when sap flow is heavy (see table below). Although unattractive, sap drainage has little negative effect on tree growth. Some of the sap dripping can be avoided by pruning in summer or at other times of the year.


Purple Leaf Scorch: The most common leaf discoloration is a purplish blotch due to the environment rather than a fungus. This leaf scorching is caused by the presence of water or ice on the leaves at the time the sun is shining brightly. This causes a scalding, followed by the invasion of secondary organisms and finally by scorching.

Spine Spot: Small, gray spots with purple halos are caused by the puncturing of the leaves by the spines of adjacent holly leaves. This “spine spot” is often confused with the slits made by the holly leafminer. Leafminer damage has neither a gray center nor a purple halo.

Winter Damage: Symptoms of winter damage may be browning of leaves, marginal leaf scorch, defoliation, twig and limb death, and death of entire plants.

Drought Damage: Holly leaves often turn yellow or brown during a sudden drought period. Japanese hollies, particularly ‘Helleri’, are not very tolerant to low soil moisture, particularly for the first several years after planting. Keep plants watered during periods of drought.

Table 1. Fungicides, Insecticides & Miticides to Control Diseases & Pests of Hollies

Caution: Pollinating insects, such as honey bees and bumblebees, can be adversely affected by the use of pesticides. Avoid the use of spray pesticides (both insecticides and fungicides), as well as soil-applied, systemic insecticides unless absolutely necessary. If spraying is required, always spray late in the evening to reduce the direct impact on pollinating insects. Always try less toxic alternative sprays first for the control of insect pests and diseases. For example, sprays with insecticidal soap, horticultural oil, neem oil extract, spinosad, Bacillus thuringiensis (B.t.), or botanical oils can help control many small insect pests and mites that affect garden and landscape plants. Neem oil extract or botanical oil sprays may also reduce plant damage by repelling many insect pests. Practice cultural techniques to prevent or reduce the incidence of plant diseases, including pre-plant soil improvement, proper plant spacing, crop rotation, applying mulch, applying lime and fertilizer based on soil test results, and avoiding overhead irrigation and frequent watering of established plants. Additionally, there are less toxic spray fungicides that contain sulfur or copper soap, and biological control sprays for plant diseases that contain Bacillus subtilis. However, it is very important to always read and follow the label directions on each product. For more information, contact the Clemson Extension Home & Garden Information Center.

If this document didn’t answer your questions, please contact HGIC at [email protected] or 1-888-656-9988.

Original Author(s)

Marjan Kluepfel, Former HGIC Horticulture Information Specialist, Clemson University
Janet McLeod Scott, Former Horticulture Information Specialist, Clemson University
James H. Blake, EdD, Extension Associate/Adjunct Professor, Dept. of Plant and Environmental Sciences, Clemson University
Clyde S. Gorsuch, PhD, Emeritus Faculty, Entomology, Clemson University

Revisions by:

Joey Williamson, PhD, HGIC Horticulture Extension Agent, Clemson University

This information is supplied with the understanding that no discrimination is intended and no endorsement of brand names or registered trademarks by the Clemson University Cooperative Extension Service is implied, nor is any discrimination intended by the exclusion of products or manufacturers not named. All recommendations are for South Carolina conditions and may not apply to other areas. Use pesticides only according to the directions on the label. All recommendations for pesticide use are for South Carolina only and were legal at the time of publication, but the status of registration and use patterns are subject to change by action of state and federal regulatory agencies. Follow all directions, precautions and restrictions that are listed.

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