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Kuroshio Extension (KE) is the most active region of oceanic change in the North Pacific Ocean, which provides an essential place for the survival of marine microorganisms. However, Vertical changes in microbial communities in the Kuroshio Extension and the mechanisms by which environmental factors drive vertical changes in community structure remain unclear. In this work, microbial diversity, abundance, and community structure of 12 water layers (from surface to bottom) at five stations were uncovered by 16S rRNA gene high-throughput sequencing. Microbial diversity and richness decreased with increasing seawater depth. Microorganisms in the euphotic zone can be well separated from other zones based on NMDS analysis. Proteobacteria (65.20%), Bacteroidota (8.48%), Actinobacteriota (5.76%), and Crenarchaeota (4.49%) accounted for a relatively large proportion and their distribution is similar in four zones. Most of microorganisms were significantly (Spearman test, p < 0.05) correlated with salinity, density, pressure, and temperature. This work enhances our understanding of vertical microbial diversity and provides insights into the pelagic microbial community structure., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Ltd. All rights reserved.)