Euthynnus (family Scombridae) is a genus of marine pelagic fish species with a worldwide distribution that comprises three allopatric species: E. alletteratus, E. affinis and E. lineatus. All of them targeted by artisanal and commercial fisheries. We analyzed 263 individuals from Atlantic and Pacific Oceans using two genetic markers, the mtDNA Control Region (350 bp) and nuclear calmodulin (341 bp). The results obtained challenge the phylogeny of this group. We found a deep genetic divergence, probably at species level, within E. alletteratus, between the North Atlantic-Mediterranean and the Tropical East Atlantic. This deep genetic divergence was tested with several species delimitation methods. This complete phylogeographic association between the North Atlantic and the Tropical East Atlantic support the hypothesis of two cryptic species. In addition, population genetic heterogeneity was detected between the North East Atlantic–Mediterranean and North West Atlantic regions. Our results indicate two scales of differentiation in what is currently considered a single population. Accordingly, for management purposes, the populations of E. alletteratus, should be divided into a minimum of three management units. On the other hand, the high level of differentiation found in E. alletteratus contrasts with the shallow genetic divergence of E. affinis and E. lineatus