Aims This study was conducted to assess the presence and extent of differences in the gut microbiota of common bottlenose dolphins depending on rearing facilities. Methods and Results Faecal samples were collected from 16 common bottlenose dolphins at three aquaria in Japan. After extracting DNA from the faeces, the V3-V4 region of bacterial 16S rRNA was amplified and sequenced using Illumina MiSeq platform. The constituent phyla of the gut microbiota were similar among aquaria; however, the most dominant phylum differed depending on the facility, and the compositions of microbiota were remarkably varied at the family level among aquaria. The alpha diversity indices tended to differ among aquaria. Some bacterial families observed in terrestrial mammalian carnivores or carnivorous fish were detected, as well as several bacterial species suspected of being pathogenic in dolphins. Conclusion Our findings indicate that captive environmental conditions including prey and housing types may contribute to differences in the gut microbiota of the dolphins. Significance and Impact of the Study This is the first study revealing the differences in gut microbiota of captive dolphins among facilities. Our findings will provide valuable information for improving the health management of dolphins.