Identifying factors shaping the intraspecific genetic diversity leads us to understand how organisms interact with their environment. In marine ecosystems, there are no obvious physical barriers for organisms to disperse, hence, gene flow is extensive and high genetic diversity is diffused among large populations. However, biogeographical barriers and environmental variables such as ocean currents and water temperature are possible factors shaping genetic diversity and population structure in marine organisms. Here, I analyzed population structure of Pacific cod (Gadus macrocephalus) sampled from across Japanese coastal area using microsatellite loci and mitochondrial DNA. There was two distinct populations observed and those populations are possibly separated at the southern part of Sea of Japan where warm current flows around the area which may be a possible factor separating populations. This study provides important backgrounds of a widely distributed ground fish around Japan. Future works in evolutionary responses to climate change lead us to reveal the adaptive shifts in species ranges and the genetic basis of adaptation.