Cryphonectria species associated with canker disease are presently difficult to identify, because of lack of ex-type cultures with molecular data and few distinguishable characters. During our survey about chestnut blight in western China, Cryphonectria parasitica was confirmed as the most important canker pathogen based on ten morphologically atypical isolates. Two novel species with orange stromata are introduced based on multigene sequence (ITS, TUB1, TUB2) analyses. This is the first study that has established the Cryphonectria species associated with oak canker in China using a multiphasic approach.