The black rockfish Sebastes schlegelii is an important fishery species in Japan, South Korea and China. In recent years, overfishing has decimated the natural resources of S. schlegelii, and the implementation of programs aimed at enhancing fish stock has been initiated. However, the genetic structure of northern populations remains elusive, posing challenges in the collection and preservation of germplasm resources. In this study, in total of 191 S. schlegelii individuals from seven populations including one cultured population (Changdao: CDYZ) and six wild populations (Liangyungang: LYG Qingdao: QD Weihai: WH Changdao: CDYS Beidaihe: BDH) sequenced by 2b-RAD method and their population genetics was analyzed using 27,064 SNPs obtained. The results indicated that the genetic diversity of the wild and cultured populations were all low (PIC < 0.25, Ho: 0.174-0.273, He: 0.173-0.234), and even the cultured populations was higher than that of the wild populations. There was a moderate degree of genetic differentiation between the cultured population and the six wild populations (0.05 < Fst < 0.25). However, the genetic differentiation was lower among the other wild populations (Fst < 0.05). The analyses of population genetic structure indicated that those wild populations clustered together first and finally with cultured populations CDYZ which clustered separately except for one individual. Therefore, scientific breeding programs and germplasm conservation can play an important role in stabilizing genetic structure. In addition, gene flow among the seven populations were high (Nm > 1). This study provides a theoretical basis for the conservation and rational utilization of germplasm resources for S. schlegelii.