How to Manage Pests

UC Pest Management Guidelines


Phytophthora Root and Crown Rot

Pathogen: Phytophthora megasperma

(Reviewed 11/06, updated 11/06)

In this Guideline:


Primary symptoms of Phytophthora root and crown rot include tan-to-brown lesions on taproots, especially where a lateral root emerges. Lesions eventually turn black while the center of the root becomes yellow. In the root interior, orange-to-reddish streaks spread up several inches from the rotted end of the roots. Lesions can appear at any depth where water drainage is impeded. Occasionally, the disease may spread to the crown from the taproot.


Phytophthora root rot is a cool season crown and root disease. It is important where soil water is excessive and can affect large areas of a field. Root and crown rot is common at the tail end of flood-irrigated fields where water collects.

The causal organism survives in soil as mycelia in infected plant tissue or as thick-walled oospores. The fungus also produces thin-walled sporangia, which release motile zoospores in the presence of free water.

If the crown becomes infected, the plant will likely die. If infection is limited, the plant may continue growing at a reduced rate, and it will be susceptible to other pests and diseases. Root and crown rot can be injurious to seedling stands but is more common in established fields.


Use resistant cultivars to keep the disease under control in areas where the alfalfa crop remains in the soil and water management are the keys to controlling Phytopthora root rot. Take the following steps to decrease the amount of time that soil is saturated with water: till deeply to reduce compaction, reduce the length of flood irrigation runs, shorten irrigation time, level land before planting, install a tailwater ditch to remove excess water, and plant on beds to help alleviate disease severity.

Be careful when using return water because this and other pathogens (and nematodes) can be carried in recirculated irrigation water. Cultivars resistant to Phytophthora root rot are listed in the current leaflet Winter Survival Fall Dormancy & Pest Resistance Ratings for Alfalfa Varieties (PDF) from the National Alfalfa Alliance Web site. Use resistant cultivars with sound cultural practices in fields known to have problems with Phytophthora.


[UC Peer Reviewed]

UC IPM Pest Management Guidelines: Alfalfa
UC ANR Publication 3430


  • R. M. Davis, Plant Pathology, UC Davis
  • C. A. Frate, UC Cooperative Extension, Tulare County

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