The Kuroshio-Oyashio confluence region of the Northwest Pacific Ocean is one of the most productive fishing areas, which is rich of fish resources. In order to understand the biodiversity of fish communities in the confluence region and to protect and exploit fishery resources properly,we used environmental DNA （eDNA） to analyze the fish diversity in the Kurishio-Oyashio confluence region during the summer. A total of 51 species of marine fishes （22 orders,30 families and 44 genera） were detected among 22 water sampling stations using high-throughput sequencing analysis. The Myctophidae family was the richest in species, comprising 33.33% of the detected fish species. In addition, the primary species with higher relative abundance were Stenobrachius nannochir, Gonostoma atlanticum, Notoscopelus japonicus, Sardinops melanostictus, Takifugu poecilonotus, Ceratoscopelus warmingii, Hexagrammos agrammus, Scomber japonicus, Nematalosa japonica and Diaphus kuroshio. The alpha diversity among stations was obviously different, and there were higher biodiversity in low-latitude sections than that of high-latitude sections. Redundancy analysis showed that the content of dissolved oxygen was the main environment factor impacting the fish species composition. The results indicated that eDNA can be a useful method for monitoring fish diversity and spatial distribution in the Kuroshio-Oyashio confluence region.