Flowering cherry trees are susceptible to a number of fungal diseases, including brown rot (also called blossom blight), black knot and Eutypa dieback. Once a tree is infected with a fungus, there's no cure. The damaged limbs must be removed and disposed of carefully away from the garden. These common fungal diseases can severely damage or kill a flowering cherry tree.
Brown rot infects the blossoms of the cherry tree just as they begin to fade in the spring. It appears first as tiny black dots on the blossoms and spreads to the limbs, moving down the limbs to the trunk. Limbs infected with brown rot must be pruned back at least 8 inches from the infection. Black knot also spreads in the spring. It overwinters inside knots on trees until the warmth and moisture of spring release and disperse the spores. It first appears on trees as corky knots that slowly turn green, then black. Black knot infection interferes with a tree's circulatory system, causing limbs to wither and die. Any knotty branches must be pruned away, at least 3 inches below the knot, during winter and early spring.
The fungus Eutypa lata causes cherry tree dieback during late spring and summer. It enters the tree in water drops through pruning-cut sites, causing limbs to suddenly wilt and die. Wilted limbs must be pruned back at least a foot from the infection. With all fungal infections, pruning equipment must be disinfected between each cut and between trees to prevent it from spreading. Fungicides can help prevent infection if used in early spring.