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Cytochrome c oxidase I (COI) and microsatellite markers were used to evaluate the genetic structure, connectivity, and evolutionary history of white mullet (Mugil curema), along locations in the Atlantic, Gulf of Mexico (GoM), and Pacific coasts. DNA sequences of 125 COI were obtained and identified as Mugil curema with 100% identification and coverage. COI sequences resulted in the formation of two haplogroups, one in the GoM along with a location in Oaxaca named Huave System (HU), belonging to the Pacific coast, and another one in Mexican Pacific (MP, with exception of the former). The evolutionary history of both haplogroups concur with the closure of the Isthmus of Panama (1.5 My). The MP haplogroup showed a subdivision in a northern group and a southern group, with a separation of 0.4 My that could be the result of a combination of Pleistocene factors and oceanographic changes following the closure of the Isthmus of Panama. Furthermore, microsatellites result also revealed that the GoM/HU haplogroup has larger genetic distances with other samples from the MP than with those of the GoM; this result was confirmed with the individual allocation analysis. The presence of Huave System mullets within the GoM lineage may be due to the confinement of individuals in this locality, that have retained ancestral polymorphisms of the GoM sister lineage, or to a recent connection. The genetic similarity of fish populations in both coasts of Mexico is a completely new report on a species that recently connected the Pacific and Atlantic coasts.