16S rRNA gene fragment from mesopelagic water collected in Nov 2013 at coastal area of Muroto city, Kochi, Japan (at a depth of 320 m) were analyzed to comprehensively reveal the bacterial community in North Pacific Intermediate Water. The goal of this study was to comprehensively reveal the bacterial community in mesopelagic water masses around Japan for the first time. For comparison, 16S rRNA gene fragments from surface seawaters around Japan were similarly analyzed comprehensively for the first time.