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In recent decades, microbial diversities in different hydrothermal regions of the Okinawa Trough have been elucidated. However, the microbial community compositions in non-hydrothermal sites in the Okinawa Trough are unclear. In this study, we analyzed the microbial communities at three different non-hydrothermal sites from two depths in the Mid-Okinawa Trough. The bacterial and archaeal diversities, which were dominated by Gammaproteobacteria and Thaumarchaeota, respectively, were similar in the surface sediments (samples CW12A, CW27A, and CW28A) and grouped together. However, the microbial communities in deeper habitats (samples CW12B, CW27B, and CW28B) were completely different. The microbial diversities in the CW12B and CW28B samples, which were significantly different from that in sample CW27B, were more closely related and grouped together. In sample CW27B, the most abundant bacterial and archaeal groups were Gammaproteobacteria and Hadesarchaea, respectively. In samples CW12B and CW28B, Firmicutes was the major bacterial phylum and the major archaeal phyla were Lokiarchaeota and Bathyarchaeota. These results indicate that the microbial community composition in relatively deep samples from non-hydrothermal fields appears to be more diverse and distinct from that in surface sediments. In addition, all the reported microbial communities at hydrothermal and non-hydrothermal sites in the Okinawa Trough region were summarized. Both the bacterial and archaeal communities are variable at the different sampling sites. Even within a location, the microbial community compositions changed with depth. Overall, our work documents the microbial diversity at different sampling sites and varying depths in non-hydrothermal fields of the Mid-Okinawa Trough. This suggests that distinct microbial community compositions likely occur beneath the sediments in different non-hydrothermal Okinawa Trough regions. [ABSTRACT FROM AUTHOR]