[Objectives]  To understand the dynamics of microbial diversity in red grapes infested by Drosophila suzukii and Drosophila melanogaster and identify microorganisms associated with these two species. [Methods]  Microorganisms in red grapes infested by D. suzukii and D. melanogaster for 2, 4, 6, 8, and 10, days were separated, purified, and identified with ITS and 16S rDNA genetic analysis. [Results]  25 species of bacteria and 7 species of fungi were identified. Microbial diversity was affected by infestation with either D. suzukii or D. melanogaster. The number of microorganism species in grapes infested by these species exceeded that in control grapes. Peak numbers of microorganism species were recorded after infestation by D. melanogaster for 4 days, and after infestation with D. suzukii for 8 days. Infestation with D. suzukii and D. melanogaster generated Geotrichum candidum. Three species of Acetobacter spp. were only cultivated from grapes infested by D. melanogaster. [Conclusion]  Infestation by D. suzukii or D. melanogaster accelerated the decay of red grapes and the generation of microorganism species, including G. candidum. Acetobacter spp. was more strongly associated with D. melanogaster than with D. suzukii. This study provides a theoretical foundation for investigating coevolution between grapes, Drosophila spp. and microorganisms.