Abstract: Roughskin sculpin, also known as Trachidermus fasciatus, is a catadromous fish that live in the seawater along the coast of the northwest Pacific Ocean. The fish population size has been largely reduced in recent years due to the deterioration of the habitats, water pollution and the construction of dams. To protect the fish resource and to improve the fishery management, we need to better understand the genetic structure of the fish population. In this study, we collected 69 individuals from 8 sampling sites near the coast of China and Japan, including Hangzhouwan (HZ), Wendeng (WD), Rongcheng (RC), Dongying (DY), Qinhuangdao (QH), Dalian (DL), Dandong (DD) and Ariake Sea (AS). The mitochondrial control region of T. fasciatus was amplified with polymerase chain reaction (PCR) technology and was sequenced with the forward and reverse primers by the automatic sequencer. We found that the 8 populations exhibited high haplotype diversity (0.978) and low nucleotide diversity (0.0079). Our analysis of the control region revealed the terminal associated sequence, the central conserved domains and the conserved sequence block domains. Moreover, the analysis of NJ phylogenetic trees and median-networks demonstrated that these populations could be divided into the Chinese lineage and the Japanese lineage. Finally, both the genetic differentiation index (Fst) and the analysis of molecular variance (AMOVA) indicated a significant genetic differentiation between the Japanese population and the Chinese populations, as well as a moderate differentiation within the Chinese populations.