Bacterial Canker. Bacterial canker is one of the most common cherry tree diseases. This condition results from two different bacteria that are related to each other. Cankers show up on cherry trees as dark depressions on the trunks and the branches and emit a substance that has a gummy texture.Bacterial canker can also show up in the form of dark-colored depressions on the skin of the fruit.ubmit. Cherry trees are flowering deciduous plants that produce the popular fruit known as cherries. Cherry trees bear light to dark red, round fruit that has smooth skin. The fruit is edible and has either a sour or sweet taste. The fruit of ornamental cherry trees tends to be smaller.