Psenopsis anomala (Japanese butterfish) is a commercially important fish species with a wide distribution in the Northwest Pacific Ocean, but its catch in Taiwanese waters has been declining for decades. This study aims to elucidate the migration pattern and population structure of P. anomala by analyzing otolith δ18O values, mitochondrial COI and cyt b sequences, respectively. The results reveal a seasonal migration pattern between the northern South China Sea and the Yellow Sea. Analysis of the haplotype network reveals that most P. anomala collected from each location share the haplotypes Hap1 and Hap5, while each population also has its own unique haplotypes. Analysis of molecular variance reveals that the primary variation (92.98%) is observed among individuals within the populations. Fu's FS test conducted for all populations showed no significant differences, and the mismatch distribution aligns with recent population expansion. Both the maximum likelihood tree and the median-joining network show no geographic population structuring in P. anomala samples from Japan and Taiwan. The combined findings from otolith microchemistry and genetic analysis suggests that P. anomala distributed in east Asia shall be managed as a single stock.