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2023–2024 Florida Citrus Production Guide: Phytophthora Foot Rot, Crown Rot, and Root Rot

Megan M. Dewdney and Evan G. Johnson

Foot rot results from scion infection near the ground level, producing bark lesions that extend down to the bud union on tolerant rootstocks. Crown rot results from bark infection below the soil line when susceptible rootstocks are used. Root rot occurs when the cortex of fibrous roots is infected, turns soft, and appears water-soaked. Fibrous roots slough off their cortex, leaving only a white thread-like stele (inner tissue of the fibrous root). Foot rot, crown rot, and root rot can be caused by Phytophthora nicotianae or P. palmivora. When managing phytophthora-induced diseases, integration of chemical control methods and cultural practices (e.g., disease exclusion with phytophthora-free planting stock, tolerant rootstocks, proper irrigation practices [see chapter 12, Irrigation Management of Citrus Trees]) is necessary. Phytophthora management with chemical control should not be considered until other potential causes of decline in tree production are evaluated and corrected. See also chapters on BlightHuanglongbing (Citrus Greening), and Nematodes. The decision to treat should follow soil sampling to determine how much phytophthora is present in the soil. Details are given below.

Cultural Practices to Manage P. nicotianae

Field locations not previously planted with citrus are probably free of citrus-specific P. nicotianae. Planting stock should be free from Phytophthora spp. in the nursery, and inspection for fibrous root rot in the nursery or grove before planting is advised. If uncertain, testing of nursery stock for Phytophthora spp. is recommended. In groves with a previous history of foot rot, consider use of Swingle citrumelo or other tolerant rootstocks (see Florida Citrus Rootstock Selection Guide) for replanting. Tolerance to Phytophthora spp. can be compromised when planted in unfavorable soils for the rootstock (e.g., Swingle citrumelo in calcareous soils). Rootstocks tolerant to foot and root rot normally do not support damaging populations once trees are established. Cleopatra mandarin should be used with caution because it is prone to develop crown and foot rot when roots are infected in the nursery or when trees are planted in flatwoods situations with high or fluctuating water tables and fine-textured soils. When resetting, never use Cleopatra mandarin in a grove with a history of damaging phytophthora, regardless of region. Plant trees with the bud union more than 6 inches above the soil line and provide adequate soil drainage. Overwatering, especially of young trees, promotes buildup of phytophthora populations in the soil and increases risk of foot rot infection. Prolonged wetting of the trunk, especially if tree wraps are used on young trees, should be avoided by using early to midday irrigation schedules. Control of fire ants prevents their nesting under trunk wraps and feeding damage to moist, tender bark, which is then susceptible to infection.

Sampling for Phytophthora Spp.

Determine population densities of the fungus-like organism in grove soils to assist decisions of whether to treat with fungicides. Collect soil samples containing fibrous roots from March to November from under the canopy within the irrigated zones. When sampling trees of average canopy condition, combine individual small amounts from the top ten inches of soil from 20 to 40 locations in the microsprinkler zones within a 10-acre block into one resealable plastic bag to retain soil moisture. Samples must be kept cool but not refrigerated for transport to an analytical laboratory. Currently, populations in excess of 10 to 20 propagules per cm3 soil of total Phytophthora spp(P. nicotianae + P. palmivora) are considered damaging. The same soil sample should be tested for populations of nematodes to assess whether they occur at damaging levels.

Chemical Control

Use of fungicides in young groves should be based on rootstock susceptibility, likelihood of Phytophthora spp. infestation in the nursery, and history of phytophthora disease problems in the grove. For susceptible rootstocks, such as Cleopatra mandarin and sweet orange, fungicides may be applied to young trees for foot rot on a preventive basis. For young trees on other rootstocks, fungicide treatments should commence when foot rot lesions develop. The fungicide program for foot rot should be continued for at least one year for tolerant rootstocks but may continue beyond the first year for susceptible rootstocks. In mature groves, the decision to apply fungicides for root rot control is based on yearly soil sampling to determine whether damaging populations of P. nicotianae occur in successive growing seasons. Timing of applications should coincide with periods of susceptible root flushes after the spring leaf flush, usually from late spring to early summer and after the fall leaf flush in October to November. Soil application methods with fungicides should be targeted to irrigated areas under the canopy with the highest fibrous root density. To avoid leaching from the root zone, soil-applied fungicides should not be followed by excessive irrigation. Aliette, phosphite salts, Ridomil Gold, or Presidio are effective, but alternation of the materials should be practiced to minimize the risk of the development of fungicide resistance. It is recommended to alternate the soil-applied Ridomil and Presidio on the major spring and fall root flushes as well as to continue to apply Aliette or phosphite salts on a calendar schedule per the label.

Larval Feeding Injury to Citrus Roots and Its Relationship to Invasion by Phytophthora Spp.

Association of phytophthora root rot with root damage by larvae of Diaprepes abbreviatus has been called the Phytophthora-Diaprepes (PD) complex (see chapter 27, Citrus Root Weevils, or the Diaprepes Root Weevil Task Force website). A far more severe interaction has been identified between P. palmivora and Diaprepes root weevil than for P. nicotianae. The damage caused by P. palmivora is often associated with poorly drained, fine-textured soils and rootstocks like Swingle citrumelo and Carrizo citrange that are normally tolerant of P. nicotianae. In the more severe form, structural roots collapse from what appears to be moderate larval damage followed by aggressive spread of P. palmivora through the structural roots.

Rootstock susceptibility to damage by the PD complex depends on which Phytophthora sp. is present and whether the soil and water conditions are conducive to the fungus-like organism or to rootstock stress. In most situations, P. nicotianae is the predominant pathogen, and Swingle citrumelo appears to perform acceptably as a replant in weevil-infested groves, provided soil conditions are suited for this rootstock (e.g., favorable pH and calcium carbonate status, sandy soil texture, well-drained, etc.). When P. palmivora is present in poorly drained soils high in clay, pH, or calcium carbonate, Diaprepes root weevils render normally tolerant Swingle citrumelo and Carrizo citrange susceptible to phytophthora root rot infection. Thus, tolerance of Swingle citrumelo is restricted to the Ridge and certain flatwoods soils. For further information about rootstock selection, refer to chapter 12, Rootstock and Scion Selection, and the Rootstock Selection Guide.

Management of the Phytophthora-Diaprepes Complex

Selection of tolerant rootstocks for replanting Diaprepes root weevil–affected groves is important for management of future losses. For existing trees, fungicides in conjunction with careful water and fertilizer management have been utilized to maintain tolerance to Diaprepes root weevil and phytophthora damage. Fertigation maximizes water and nutrient uptake efficiency by roots in well-drained soils. However, use of fertigation to regenerate roots is limited in poorly drained soils and high water tables typical in the flatwoods. In these situations, there may be increased reliance on fungicides to control root damage by Phytophthora spp.

Based on studies of the PD complex, aggressive control of Diaprepes root weevil larvae and adult stages should be implemented as soon as infestation is discovered to minimize the more severe phytophthora damage that follows larval feeding on roots. The IPM program may include carefully scheduled fertigation in well-drained soils to promote regeneration of fibrous roots after damage. In the flatwoods, IPM may include use of fungicides under the following conditions: (1) the soils are fine textured, poorly drained, high in pH, or calcareous, (2) the trees are on rootstocks susceptible to either or both Phytophthora spp., and (3) populations are above the damaging levels (10 to 20 propagules per cm3 soil). A key to assist growers making Phytophthora-Diaprepes management decisions is available at the Diaprepes Root Weevil Task Force website as well as the Citrus Rootstock Selection Guide.

Management of the Phytophthora-HLB Interaction

Management of phytophthora root rot is complicated by huanglongbing [HLB; see chapter 29, Huanglongbing (Citrus Greening)] because the causal bacterium infects all parts of the citrus tree, including the roots. HLB accelerates phytophthora infection and fibrous root damage. HLB predisposes roots to P. nicotianae infection apparently by increasing attraction of zoospores to roots, accelerating infection, and lowering resistance to root invasion. The spread of HLB has led to more frequent cases of damaging phytophthora populations. Most recently, there has been a multiyear cycling of phytophthora populations apparently associated with lower fibrous root density and bursts of root growth as trees continue to decline from HLB. This has heightened concern for the root health of HLB-affected trees and initiation of measures to reduce root stress, which includes Phytophthora spp., citrus nematodes, Diaprepes, and abiotic soil factors. While all of these factors need to be considered and assessed on a case-by-case basis depending on site and rootstock, specific factors must be considered when controlling phytophthora with high-incidence HLB.

Although HLB causes fibrous root dieback, it also increases new growth of fibrous roots. Similar to leaf flushing, new root growth is no longer as synchronized into flush events. This is important because phytophthora preferentially infects new root growth. Constant availability of new root growth is a likely cause of the rapid development of damaging phytophthora populations under favorable conditions. The cycles of root dieback and root flushing caused by HLB leads to large swings in phytophthora propagule counts in a grove. Preliminary data indicate that chemical management has reduced effectiveness for control of Phytophthora spp. and prevention of root loss. Therefore, it is important to monitor phytophthora propagule counts before major summer and fall root growth events. If a damaging population is developing, it is important to time chemical applications to protect those major root flushes.

Web addresses for links:

Diaprepes Root Weevil Task Force:

Citrus Rootstock Selection Guide:

Irrigation Management of Citrus Trees chapter:

Group 4 fungicides (metalaxyl and mefenoxam) are not recommended for phytophthora control in citrus nurseries.

Recommended Chemical Controls


See Tables 1 and 2.

Rates for pesticides are given as the maximum amount required to treat mature citrus trees unless otherwise noted. To treat smaller trees with commercial application equipment including handguns, mix the per-acre rate for mature trees in 250 gallons of water. Calibrate and arrange nozzles to deliver thorough distribution, and treat as many acres as this volume of spray allows.

Table 1. 

Recommended chemical controls for phytophthora foot rot, crown rot and root rot—fosetyl AL and phosphite salts products.

Table 2. 

Recommended chemical controls for phytophthora foot rot and root rot—mefenoxam and copper products.


Publication #PP-156

Date: 8/15/2023

Related Experts

Johnson, Evan G.

University of Florida

Dewdney, Megan M.

University of Florida

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The use of trade names in this publication is solely for the purpose of providing specific information. UF/IFAS does not guarantee or warranty the products named, and references to them in this publication do not signify our approval to the exclusion of other products of suitable composition.

Use pesticides safely. Read and follow directions on the manufacturer's label.


About this Publication

This document is PP-156, one of a series of the Plant Pathology Department, UF/IFAS Extension. Original publication date December 1999. Revised annually. Most recent revision June 2023. Visit the EDIS website at for the currently supported version of this publication.

About the Authors

Megan M. Dewdney, associate professor, and Evan G. Johnson, former research assistant scientist, Plant Pathology Department; UF/IFAS Citrus REC; UF/IFAS Extension, Gainesville, FL 32611.


  • Megan Dewdney