Agriculture: Citrus Pest Management Guidelines

Alternaria Rot

  • Alternaria citri
  • Symptoms and Signs

    Alternaria rot is a fungal disease that affects mainly navel oranges and lemons. Fruit infected with Alternaria change color prematurely. The decay is softer on lemons than on oranges. Infections typically occur in the grove; disease often doesn't develop until after harvest, and most damage occurs during storage. On navel oranges, the disease is also called black rot, and results in dark brown to black, firm spots or areas at the stylar (blossom) end or in the navel. If you cut the fruit in half, you can see the rot extending into the core.

    Comments on the Disease

    There are many strains of the pathogen Alternaria citri. The strain that causes Alternaria rot is a non-toxin-producing strain. Toxin-producing strains that produce other diseases of citrus have not been reported in California. Strains on mandarin causing brown spot have been referred to as A. alternata pv. citri.


    • Prevent stress to reduce the incidence of splitting and Alternaria rot. Healthy, good quality fruit are more resistant to Alternaria rot than stressed or damaged fruits. Stylar-end infections generally occur on orange cultivars with poorly formed navels.
    • Preharvest fungicide applications are usually ineffective.
    • Delay harvest until infected fruit have fallen to prevent inadvertent inclusion of infected fruit in the harvested crop. However, unaffected fruit should be harvested at optimum maturity.
    • Postharvest sprays with imazalil, azoxystrobin, fludioxonil, or mixtures of these may provide partial control.
    Common name Amount to use REI‡ PHI‡
    (Example trade name) (hours) (days)
    Not all registered pesticides are listed. The following are ranked with the pesticides having the greatest IPM value listed first—the most effective and least likely to cause resistance are at the top of the table. When choosing a pesticide, consider information relating to the pesticide‚Äôs properties and application timing, honey bees, and environmental impact. Always read the label of the product being used.
      (Graduate A+) 32–64 oz/100 gal water or 250,000 lb fruit NA NA
      MODE-OF-ACTION GROUP NAME (NUMBER1): Phenylpyrrole (12) and quinone outside inhibitor (11).
      COMMENTS: Use as a dip, drench, flood, or spray.
      (Graduate) 16–32 oz/100 gal water or 250,000 lb fruit NA NA
      MODE-OF-ACTION GROUP NAME (NUMBER1): Phenylpyrrole (12)
      COMMENTS: Use as a dip, drench, flood, or spray.
      (FungaFlor 500EC) Label rates NA NA
      MODE-OF-ACTION GROUP NAME (NUMBER1): Demethylation inhibitor (3).
    * Permit required from county agricultural commissioner for purchase or use.
    Restricted entry interval (REI) is the number of hours (unless otherwise noted) from treatment until the treated area can be safely entered without protective clothing. Preharvest interval (PHI) is the number of days from treatment to harvest. In some cases, the REI exceeds the PHI. The longer of two intervals is the minimum time that must elapse before harvest.
    1Group numbers are assigned by the Fungicide Resistance Action Committee (FRAC) according to different modes of actions. Fungicides with a different group number are suitable to alternate in a resistance management program. In California, make no more than one application of fungicides with mode-of-action group numbers 1, 4, 9, 11, or 17 before rotating to a fungicide with a different mode-of-action group number; for fungicides with other group numbers, make no more than two consecutive applications before rotating to fungicide with a different mode-of-action group number.
    NA Not applicable.
    Text Updated: 01/19
    Treatment Table Updated: 01/19