Thirty-eight strains of Colletotrichum were isolated from diseased Citrus leaves in Guizhou and Yunnan provinces in China. Based on morphological characters and multilocus sequence data, the strains were identified as C. boninense (1 strain), C. brevispora (1), C. fructicola (2), C. gloeosporioides (29), C. karstii (2), C. simmondsii (1) and Colletotrichum murrayae; the latter represents a new species which is described in this paper. Colletotrichum gloeosporioides was originally isolated from Citrus sinensis in southern Italy and was the most common species associated with diseased leaves of Citrus in China.