There are black spots on the surface of my apples. Can I eat the skins?

Question: 

There are black spots on the surface of my apples. Can I eat the skins?

Answer: 

The black spots are probably sooty blotch or flyspeck.  Sooty blotch and flyspeck are two different fungal diseases that often occur together on apples.  Sooty blotch appears as dark brown to black, ½ inch or larger smudges on the surface of the apple.  Flyspeck produces clusters of shiny, round, black dots.  Individual dots are about the size of a pinhead.  Environmental conditions that favor disease development are moderate temperatures and extended wet periods in late summer/early fall.

Sooty blotch and flyspeck live on the surface of the fruit.  Damage is mainly cosmetic.  The skins on the apples can be eaten, they just don't look very appetizing. 

Cultural practices and fungicides can help control sooty blotch and flyspeck.  Proper pruning of apple trees and thinning of fruit promote drying and help reduce disease severity.  Fungicides may also be necessary. 
 

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