This study investigates the influence of marine habitats (i.e., the intertidal zone, supralittoral zone, and seawater), and polymer types (i.e., polyethylene, PE; polyethylene terephthalate, PET) on the diversity and structure of bacterial communities in marine microplastics. A three-month exposure experiment was conducted in Zhairuoshan Island, Zhoushan, China, a typical caldera volcanic island with minor anthropogenic disturbances. At the end of the exposure period, the transition for peaks corresponding to oxidized groups was observed using micro-Fourier transform infrared spectroscopy. Damages, including pits and cracks, and microorganisms were observed on the surfaces of the PE and PET pellets using scanning electron microscopy. Next-generation amplicon sequencing of the bacterial communities that had colonized the microplastics revealed that bacterial composition significantly varied depending on marine habitats and exposure times, rather than polymer type. Plastic debris in the intertidal zone exhibited the highest bacterial richness and diversity, and Bacillus was considered a potential degrader of plastic debris. The findings demonstrate that bacterial communities that colonize on microplastics are more potentially shaped by marine habitat and exposure time, and this would deepen our understanding of the ecological niche of microplastics surface.