Epinephelus itajara is one of the marine fish species most threatened for extinction and it is considered to be "critically endangered" by the IUCN. The present study evaluated the genetic diversity of the species and the genetic/evolutionary relationships of its populations along the Atlantic coast of South America. The results indicate relatively reduced genetic variation, re-emphasizing the low adaptive potential of the species. One of the populations presented relatively high degrees of genetic diversity and it is evolutionary isolated from the all other populations. The evidences indicate the existence of two Evolutionarily Significant Units comprising E. itajara in the Atlantic coast of South America and the conservation prospects for the species must take these evidences into account. Highlights ► A low genetic diversity was confirmed in Epinephelus itajara. ► The species is divided into two genetic/evolutionary lineages. ► A possible ESU of E. itajara occurs at the Babitonga bay (Southern Brazil). ► Physical oceanography explains the isolation at the Babitonga bay (Southern Brazil). ► Also a panmictic population occurs in the rest of the Atlantic coast of South America.

Cobia (Rachycentron canadum) is a coastal pelagic migratory fish species of tropical and subtropical waters, where it is an important game fish and it has been commercially expanded in offshore aquaculture systems. Understanding population connectivity is of utmost importance to the sustainable use and conservation of aquatic resources, and information on genetic diversity and structure is key element in unraveling differentiation when no clear physical barriers exist. In the present study, cobia genetic diversity and structure were depicted using mitochondrial DNA cytochrome b sequencing and microsatellite genotyping in samples from the Southwestern Atlantic and showed that a major single population inhabits the southern hemisphere. Cytochrome b sequencing also suggested that the Indian Ocean is the center of origin for this species' diversification. A hierarchical analysis of AMOVA compared sampling locations from the Northwestern Atlantic (from a previous study) with the Southwestern ones using nine shared microsatellite markers. Differentiation among groups (FCT = 0.41), Bayesian clustering analysis, and complementary ordination analyses (by discriminant analysis of principal components [DAPC] and factorial correspondence analysis [3D‐FCA]) presented a clear separation between the two hemispheres, supported by a Lagrangian model that explained the ocean dynamics over larval retention on the Western Atlantic. Another genetic subgroup intermingled with the main Southwestern group may also exist further south, probably associated with the Vitória‐Trindade Ridge and the local current systems. The distribution of this species in metapopulations is of extreme relevance for fisheries and fish hatcheries management in the Atlantic Ocean.