Phylogenetic relationships were determined for 45 Colletotrichum isolates causing anthracnose disease of chili in Queensland, Australia. Initial screening based on morphology, ITS and TUB 2 genes resulted in a subset of 21 isolates being chosen for further taxonomic study. Isolates in the C. acutatum complex were analysed using partial sequences of six gene regions ( ITS , GAPDH , ACT , CHS ‐1 , TUB 2 and HIS 3 ), and in the C . gloeosporioides complex were analysed using four gene regions ( ITS , TUB 2 , ApMat and GS ). Phylogenetic analysis delineated four Colletotrichum species including C. siamense , C. simmondsii , C. queenslandicum , C . truncatum and a new Colletotrichum species, described here as C. cairnsense sp. nov. This is the first reported association of C. queenslandicum , C. simmondsii and C. siamense with chili anthracnose in Australia; these species were previously associated with anthracnose on papaya and avocado. Furthermore, the dominant species causing anthracnose of chili in Southeast Asia, C. scovillei , was not detected in Australia. Inoculations on chili fruit confirmed the pathogenicity of C. cairnsense and the other four species in the development of chili anthracnose in Australia.