The work aims to explore the composition of microbial flora attached to the peach fruits of different varieties in Guizhou (a province in China). Taking Zhenyuan red peach, Yanhong peach and Yuping yellow peach as test materials, high-throughput sequencing technology was used to analyze the microbial diversity of different peach varieties in Guizhou. The results showed that the main dominant bacterial genera of red peach were Pantoea, Sphingomonas and Pseudomonas, and the dominant fungal genera were Cladosporium, Alternaria and Aspergillus; The dominant bacterial genera of the brilliant red peach are Bacteroides, Blautia and Methylobacterium, the dominant fungal genera are Monilinia, Cladosporium and Alternaria; The dominant bacterial genera of the yellow peach are Methylobacterium, Sphingomonas and Corynebacterium, and the dominant fungi are Cladosporium, Monilinia and Alternaria. In addition, α diversity analysis showed that the fungal diversity of red peach was the highest, and followed by yellow peach, β diversity analysis showed that there were significant differences in the community composition of different peach varieties, while the community composition of yellow peach and red peach was more similar. This study preliminarily defined the microbial diversity of different peach fruits in Guizhou and provided a theoretical basis for green production, storage and preservation of different peach fruits.