Taking healthy and diseased fruits of Trichosanthes kirilowii as the test material,next generation sequencing(NGS)technology and molecular identification method were used to analyze the healthy and diseased fruits to explore the species of pathomycete of T.kirilowii fruits,in order to provide reference for scientific prevention and control of diseases in Trichosanthes kirilowii.The results showed that a total of 8 phyla,24 orders,54 classes,133 families,206 genera,and 286 species were obtained from all samples.Among them,the top five genera were Diaporthe,Cladosporium,Stagonosporopsis,Colletotrichum and Hannaella.There was a high concentration of microorganisms on the diseased fruits,and the microbial community structure was significantly different from the healthy group.The microorganisms with high abundance were mainly Diaporthe and Colletotrichum.The fungus of Trichosanthes kirilowii Maxim,were isolated and purified.Four typical strains were selected for DNA molecular identification.The results showed that the fungi were Colletotrichum,Diaporthe,which verified the results of microbial diversity analysis.In summary,Diaporthe and Colletotrichum fungi were identified as the pathomycete causing the disease of T.kirilowii in Qianshan city.