The origin and maintenance of marine biodiversity remain poorly understood, particularly in highly connected oceanic environments where extensive dispersal is expected to limit population differentiation. Evolutionary processes driving population divergence or speciation frequently depend on a proper knowledge of species' life history and its interaction with major environmental variables. Using a genome-wide approach, we investigated the global population structure of the cosmopolitan pelagic fish Coryphaena hippurus Linnaeus, 1758, generating a dataset of 8.7 million SNPs and complete mitochondrial genomes. Our results reveal, for the first time, four genetically differentiated populations, corresponding to major oceanic basins: Atlantic, Pacific, Indian and Mediterranean Sea. The Mediterranean population exhibited a distinct genomic signature, likely resulting from historical isolation and restricted contemporary exchange through the strait of Gibraltar. Despite this structure, genome-wide analyses uncovered extensive signals of historical connectivity among basins. D-statistics and f4-ratio tests detected significant excess allele sharing, particularly between Indo-Pacific and Atlantic populations, while phylogenetic network reconstruction in TreeMix supported multiple migration events, highlighting the role of ancestral gene flow in shaping global genetic patterns. At finer scales, a limited but significant intra-oceanic structure was detected within both Atlantic and Pacific basins. Seascape genomic analyses revealed that environmental gradients such as salinity, phosphate concentration, light availability (PAR, Kd), and pH are significantly associated with genomic variation, suggesting that ecological factors contribute to population differentiation across heterogeneous marine environments.
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