A healthy habitat is of great significance for the fish-stock recovery. But the habitat condition of large yellow croaker (Pseudosciaena crocea), which is suffering from wide stock degradation, has not been sufficiently researched. Given the biogeochemical functions of microorganisms, the structure and functional diversity of the bacterioplankton community could be regarded as bio-indicators assessing the surrounding environmental conditions of habitat. Here, we used 16S rRNA gene high-throughput sequencing and functional prediction analysis to investigate the bacterioplankton communities in an overwintering ground for the P. crocea during the overwintering period (November 2018 to April 2019).