Fly speck and sooty blotch are surface blemish diseases caused by fungi that commonly appear together on apple or pear in late summer and fall. Although these diseases may shorten the storage life of fruit due to increased water loss, they do not cause decay, and losses are attributed to unacceptable appearance. During wet growing seasons, losses of 25% or more are commonly found even in orchards treated with fungicides. Many fungi are involved in this complex of pathogens, including Peltaster fructicola, Geastrumia polystigmatus, Leptodontium elatus, and Zygophiala jamaicensis. For more information, read this article on Sooty Blotch and Fly Speck in Apple.
Answer provided by Alan R. Biggs, West Virginia University.