Our knowledge about microbial communities through water injection-production systems of oil reservoirs is currently lacking. However, it is an ideal way to reveal the effects of habitat filters (environmental factors and dispersal limitation) on microbial community assemblage in oil reservoirs. Here, 46 samples were collected from multiple independent water injection-production systems (combined station, water injection station, wellhead and downhole of injection well, and production well) of an oil reservoir, and the communities were analyzed by 16S rRNA gene sequencing.