Blue (Scomber australasicus) and chub mackerel (Scomber japonicus) occur sympatrically in the western North Pacific. Blue mackerel were previously classified as a subspecies of S. japonicus based on morphological similarities. The practical management unit for blue mackerel is contentious owing to incomplete resolution by biological analyses. We used rapidly evolving microsatellites and slow-changing mitochondrial cytochrome b (mtCyt-b) markers to examine the phylogeographic relationships of the two species across four major hydrographic regions of the western North Pacific. Genetic variability was high in each hydrographic region and in the putative species unit, and Hardy–Weinberg equilibrium tests confirmed that blue and chub mackerel are separate genetic components. Population genetic and multiple-dimensional scaling analyses of the genotypes indicated clear genetic differences, and phylogenetic analyses of the mtCyt-b haplotypes showed a level of genetic divergence (FST=0.038, p < 0.001) consistent with separation of the two species. Based on the coalescence theory, the difference in mtCyt-b genes was small, indicating incipient speciation between blue and chub mackerel, with a diversification time of 1.9 million years ago (mya) during the Pleistocene when the East China Sea (ECS) and the South China Sea (SCS) were separated physically. Significant differences between populations of blue mackerel in the ECS and SCS were also found. Our findings confirm that blue mackerel is a valid biological species and that its populations in the ECS and SCS should be considered separate fishery stocks and conservation units for management.