The almaco jack Seriola rivoliana is a circumtropical pelagic fish of importance both in commercial fisheries and aquaculture. To understand levels of genetic diversity within and among populations in the wild, population genetic structure and the relative magnitude of migration were assessed with mtDNA sequence data and SNPs from individuals sampled from locations in the Pacific and Atlantic Oceans. A total of 25 variable sites of COI and 3,678 neutral SNPs were recovered. Three genetic groups were identified with both marker types distributed in different oceanic regions: Pacific‐1 in central Pacific, Pacific‐2 in eastern Pacific and Atlantic in western Atlantic. However, analysis of SNP identified a fourth population in Pacific coast of Baja California Sur, Mexico (Pacific‐3), while mtDNA did not. This mito‐nuclear discordance is likely explained by a recently diverged Pacific‐3 population. In addition, two mtDNA haplogroups were found within the western Atlantic, likely indicating that the species came into the Atlantic from the Indian with historical gene flow from the eastern Pacific. Relative gene flow among ocean basins was low with r m < 0.2, while in the eastern Pacific was asymmetric, and higher from south to north (r m > 0.79). The results reflect the importance of assessing genetic structure and gene flow of natural populations for the purposes of sustainable management.