Since marine environments offer few barriers to dispersal and genetic connectivity, mechanisms underlying diversification and maintenance of biodiversity for marine fishes have long been questioned. Rockfishes (genus Sebastes) are known for an extreme species diversity with approximately 110 species in the North Pacific including Japanese coasts. However, their biogeographic features and spatial diversities are poorly understood. In this study, we explored their biogeography along the coasts of northern Japan using an environmental DNA (eDNA) approach. We developed a genus-specific eDNA metabarcoding assay and applied it to eDNA samples collected from northern Japanese coasts. As a result, a total of 14 Sebastes species were detected from 36 sites. The rockfish assemblages were moderately different along with a latitudinal gradient. Based on a non-metric multidimensional scaling analysis, we found that the occurrences of several species were significantly associated with the regional dissimilarities of the assemblages. Moreover, closely related species exhibited similar distribution patterns, suggesting niche conservatisms due to their recent speciation. Further examinations for relationships between their biogeographic features and detailed environmental information will be needed to understand the mechanisms of diversification and coexistences for the rockfishes.