Some common citrus fruit diseases are brown rot, alternaria rot, blue and green mold, and anthracnose. Citrus fruit diseases are typically caused by fungi, but some infections are bacterial.
Brown rot infections are caused by the Phytophthora genus of fungi. The fungi infect the fruit through spores in the soil, so the observable decay occurs mostly on the bottom side of the fruit. Infected fruit develops a soft, dark decay. Brown rot is the most common type of fruit rot in orchards.
Alternaria rot, also known as black rot on navels, develops mostly during storage, but is identifiable when fruits are picked. Infected tissue appears dark brown or black. Alternaria rot is often relatively firm on navels, but makes lemon rinds soft. The rot extends from the rind to the core of the fruit.
Blue and green mold causes soft, watery spots in citrus rinds. In its early stages, it is often called "clear rot," because it is difficult to detect when fruit arrives at the packhouse. As the infection develops, white mycelia and blue or green spores appear on rinds.
Anthracnose causes a brown, soft decay on fruit. It can also cause discolored streaks on the rind, called "tearstaining." Colletotrichum gloeosporioides and other fungi cause anthracnose. Insecticidal soap can lead to especially severe anthracnose infections.