Cherry postharvest anthracnose (CPA) is an important fungal disease that endangers cherry production. To characterize the pathogen diversity, 43 Colletotrichum isolates were isolated from 175 cherry fruits. The multi-locus phylogenetic analysis (ACT, CAL, CHS-1, GAPDH, HIS3, ITS, TUB2) revealed that strains of the C. gloeosporioides species complex (CGSC) associated with CPA included C. aenigma, C. fructicola, C. gloeosporioides, C. siamense, and strains of the C. acutatum species complex (CASC) included C. fioriniae, C. godetiae, C. salicis. There were significant differences in biological characteristics between CGSC and CASC. The mycelium growth rate, sporulation and conidial germination ability of CGSC was significantly higher than that of CASC. However, CASC was more adaptable to low temperatures. CGSC was more pathogenic than CASC toward cherry fruits. On other tested hosts, all species showed pathogenicity only on wounded condition and the pathogenicity of CGSC and CASC to other host fruits was significantly different too. C. aenigma and C. siamense exhibited significantly higher pathogenicity towards grapes and blueberries compared to C. gloeosporioides and C. fioriniae, while the pathogenicity to cherry tomatoes was reversed. In general, CGSC was more pathogenic than CASC to testes hosts. Our results showed that there were seven species of two species complex of Colletotrichum responsible for CPA in China, and the biological characteristics and pathogenicity of different species were significantly different.