The fungal species in Colletotrichum genus are important pathogens of black pepper (Piper nigrum) to cause dieback of leaves and branches. The black pepper anthracnose has been observed frequently in Hainan, which is the main production area of black pepper in China. Thirty-six isolates from diseased leaves were collected through different fields located in six main production areas of Hainan. Twenty-three isolates were found related to black pepper anthracnose and were identified as Colletotrichum spp. through morphological characteristics and ITS information via BLAST search. All isolates collected in this study belonged to Colletotrichumgloeosporioides complex. Six genes including ITS, TUB2, CHS-1, ACT, GAPDH and ApMat were amplified and sequenced. C. siamense,C. fructicola, C. arecicola, and C. kahawae were identified as the main pathogens based on the multi- gene phylogenetic analysis and morphological characters. This is the first report of these four isolates associated with black pepper anthracnose in Hainan, China.