The gut bacterial diversity of Japanese seabass () reared in nearshore net pens at Zhoushan were analyzed by high-throughput sequencing on an Illumina MiSeq platform. The Japanese seabass were fed raw fish, and the giant croaker were fed formulated feed. The bacterial composition of the formulated feed and the seawater in the net pens were also analyzed. A total of 886 operational taxonomic units (OTUs), belonging to 8 phyla and 40 genera, were identified from the fish guts, formulated feed, and seawater. A total of 550 OTUs, belonging to 5 phyla and 15 genera, were identified from the guts of the Japanese seabass and giant croaker. At the phylum level, Firmicutes dominated in the fish gut, while at the genus level, Bacillus dominated in giant croaker. Similarities in the bacterial communities were higher between guts of different fish species than between fish gut and the seawater in the net pen. This suggests that gut bacterial communities of Japanese seabass and giant croaker are independent of the seawater in the net pens. There were more common OTUs between the giant croaker gut and the formulated feed than between the giant croaker gut and the seawater, suggesting a greater impact of the feed on the intestinal bacterial community.