Morphological and phylogenetic approaches were employed to examine the diversity of 58 Cytospora specimens collected from different regions of Shanxi Province in northern China. The results showed presence of five morphological groups according to characteristics of fruiting body, spore shape and pure cultures. Three different algorithms were used to construct phylogenetic trees based on sequences of a single gene (ITS) and three genes (ITS, LSU and TEF), which showed that Cytospora from Shanxi could be clustered into five separate clades, further supporting the morphological results. The five groups were identified as C. carbonacea, C. chrysosperma, C. leucostoma, C. mali and C. sophorae, which were isolated from 11 different hosts of five cities of Shanxi Province. The hosts Crataegus pinnatifida, Euonymus bungeanus, Fraxinus chinensis and Magnolia grandiflora were found for the first time associated with Cytospora canker, which is critical to the disease prevention and treatment, and subsequent studies of pathogen pathology.