What you see: Black smudgy spots on apple skin
What it is: A fungus called sooty blotch
Eat or toss? Eat! You’re seeing a cosmetic issue, not anything that will hurt you. You can also quite easily rub or rinse off the sooty stuff.
This apple may look like it just took a bath in charcoal, and it may have a fungal disease called "sooty blotch," but don't abandon it just yet. You're looking at a cosmetic issue, and nothing more.
This fungus only inhabits the apple's natural wax, on the outermost layer of the fruit. In fact, the sooty blotch fungus likes wax so much it can live on wax paper, says Rich Marini, a horticulture professor at Pennsylvania State University. Which all means that the fungus isn’t in the apple’s crispy flesh. So, if you rub or wash off the black stuff, or peel the apple, you’ll never know it was there. Or, you could follow Marini's lead and sink your teeth in.
“I’ve eaten a lot of it,” Marini says. “It’s not harmful to human health and you can’t really taste it.”
Sooty blotch is common and often pops up in residential trees and on organic orchards where fungicides aren’t used, Marini says. It tends to be worse in humid areas. Even on a single tree, it will be concentrated more on what’s literally the low-hanging fruit, because the lower branches, which get less sunlight, are wetter.
Rich Marini - Professor of Horticulture - Pennsylvania State University
Yard and Garden: Apples and Pears - Iowa State University Extension and Outreach
Sooty Blotch and Fly Speck of Apples - Royal Horticultural Society
Sooty Blotch in Apples Not a Health Concern -- MissouriFamilies.org.