Remove any old or wild plum or cherry trees growing nearby, as well as any seedlings as they appear. Alternatively, avoid planting the chokecherry downwind from old plantings. Minimizing potential sources of innoculum is essentially the only way to prevent black knot infections altogether. All other efforts focus on eliminating the disease where it is found and preventing its spread.
Inspect the chokecherry tree regularly beginning in late winter or early spring before bud break. Look for any twigs or young growth that have warty swellings. Knots first appear corky and olive-green but turn black and brittle with age.
Prune off infected portions of the chokecherry, making any cut at least 3 to 4 inches below the visible bottom of an infection. Whenever possible, position your cut just above a bud or branch junction, or next to a branch collar, the area of raised tissue where the branch you are pruning off meets a larger branch or the trunk.
Disinfect pruning tools between pruning sessions and, if you are making cuts to remove diseased parts of the chokecherry, after each cut, by soaking the tool in a household disinfectant for about five minutes, then letting it air dry or rinsing it with clear water before making another cut.
Dispose of the infected wood you pruned off of the chokecherry immediately by removing the wood from the site. Diseased wood pruned from the tree can continue to release spores for months after it is removed. Do not put it in your compost pile.
Monitor the chokecherry throughout the growing season, and prune off and dispose of any black knot infections you find.