Abstract: ObjectiveIn order to provide theory basis for controlling pod rot of Moringa oleifera, the pathogen was i-dentified, and its taxonomic status was studied. MethodThe infected M. oleifera pods with black particles were collected from M. oleifera planting base in Xishuangbanna, Yunnan province. Based on disease symptom observation, morphological characteristics of pathogen, pathogenicity, rDNA-ITS and β-tubulin gene sequence analysis, the pathogen causing pod rot of M. oleifera was identified. ResultThe conidia of pathogen were aseptate, hyaline, smooth, curved with tapered ends and a truncated base, and ranged from 15.7-22.1 μm×2.5-4.3 μm in size. Chlamydospores were dark brown, thick-walled, and fascicled or catenulate. The gene sequences of ITS and TUB2 gene showed 99% homology with Colletotrichum chlorophyti strain IMI103806 (ITS accession number: GU227894; TUB2 accession number: GU228188). Multi-gene phylogenetic analysis showed that the tested strain had the closest genetic relationship with C. chlorophyti. ConclusionC. chlorophyti can cause pod rot of M. oleifera, which is pathogen damaging pod of M. oleifera.