Although recent studies reported taxonomic distributions of prokaryotes using few abyssal and hadal sediment samples, taxonomic heterogeneity through different ocean area and the two oceanographic layer have been not well characterized. In this study, we carried out small subunit ribosomal RNA (SSU rRNA) gene tag sequencing of a total of 92 sediment samples from seven abyssal and five hadal cores collected from three trenches in the northwest Pacific Ocean the Mariana, the Izu-Ogasawara, and the Japan trenches.