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The Gulf of California (GC) is an interior sea with a dynamic history during its formation and a contemporary environmental and oceanographic complexity; hence, it is a suitable system to test the effect of historical and contemporary factors on genomic diversity in marine species. We investigated the genomic seascape of the redhead goby (<jats:styled-content style=\"fixed-case\"><jats:italic>Elacatinus puncticulatus<\/jats:italic><\/jats:styled-content>; Ginsburg, 1938), a cryptobenthic marine fish, to gain insights into the historical and contemporary drivers shaping its population structure in the GC. A total of 4802 SNPs markers were analysed, with 3775 loci classified as neutral markers and 27 as outlier markers potentially under selection. Both markers demonstrated population structure, with the neutral markers showing two main groups corresponding to northern and southern locatities. 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