Fungal pathogens causing rot disease of purple passion fruit in Guizhou were isolated, morphology and molecular identification showed 15 pathogen strains belonged to Lasiodiplodia brasiliensis, Fusarium proliferatum, Diaporthe tectonendophytica, Diaporthe unshiuensis, D. tectonae and D. hubeiensis. Pathogenicity study revealed that 1 strain showed weak virulence, 4 strains showed moderate virulence, 4 strains showed fairly strong virulence, and 6 strains showed strong virulence. Lasiodiplodia brasiliensis strain BXG-Z-1 and D. hubeiensis strains showed strong virulence. Diversity analysis of fungal communities at different periods of development of purple passion fruit showed that fungal community OTUs of purple passion fruit in fruit flowers, young fruits and mature fruits were 26, 23 and 20 respectively, while simpson index ranged from 0.095 to 0.113, which indicated low richness of fungal community. Shannon index of all samples was below 0.5, indicating low evenness of fungal community, and correspondingly, relative abundance of Microdium spp. exceeded 90% at different growth period of passion fruit. However fungi with low relatively abundance have significant changes during different growth periods of purple passion fruit: relative abundance of Cladosporium spp., and Ruinenia spp. in the flower stage of passion fruit were the highest, and decreased to the lowest in young fruit stage, and increased again in mature fruit stage, while relative abundance of Trichoderma spp., Bipolaris spp., Amanita spp., Monilinia spp. and Cercospora spp. in flower stage were significantly higher than that in young fruit stage, and further decreased to the lowest at maturity stage.