Flying fox (Pteropus hypomelanus) belongs to the frugivorous bats, which play a crucial role in maintaining proper functioning of an ecosystem and conservation of environment. Bats are well known carriers of pathogenic viruses such as BatCov RaTG13 from the coronavirus family that share 90.55% with SARS-CoV-2, the pathogen causing recent global pandemic coronavirus disease 19 (COVID-19). However, bats’ possible role as a carrier of pathogenic bacteria is less explored. Here, using metagenomic analysis through high-throughput sequencing, we explored the gut microbiome composition of different island populations on the east and west coasts of Peninsula Malaysia. The 16S rRNA gene in samples from Redang Island, Langkawi Island, Pangkor Island and Tinggi Island was amplified. Bacterial community composition and structure were analyzed with α and β diversity metrics. In contrast to recent studies of host-microbe associations in other mammals, we found no correlation between host phylogeny and bacterial community dissimilarity across four island populations. Our analyses suggest that the significant linear relationship between Redang Island and Langkawi Island implies high bacteria diversity which supporting latitudinal correlation. We found geographic locality is a strong predictor of microbial community composition and observed a positive correlation between ecological features and bacterial richness.