The role of microbiome in the environmental adaptation in Brachyuran crabs is not actually fully uncovered. In this study we performed the analysis of the bacterial community using a short-reads approach (16S targeted-metagenomics) of the anterior and posterior anatomical section of the gills in eight different Brachyuran crab species sampled from Hong Kong area. In this study eight different crab species with four different respiration systems were considered. We found that bacterial diversity and composition were primarily influenced by the crab species within the same respiration category. Only in specific cases (eg crabs with bimodal respiration) the bacterial communities showed a differentiation between the anterior and posterior anatomical sections. This study provides new insights into the development of gill bacterial communities in Brachyuran crabs contributing to the understanding of the adaptation processes of Brachyuran crabs to different environments.