The high diversity and distribution of Bathygobius Bleeker, 1878 makes it an excellent group to study evolution patterns within the Atlantic. Thus, the aims of this work were to investigate the taxonomic status, geographical distribution and evolutionary history of Bathygobius in the Atlantic and to examine the genetic structure and demographic and phylogeographic history of two species widely distributed in the Atlantic, Bathygobius soporator and Bathygobius geminatus. Our results indicate that a new insular species, Bathygobius brasiliensis sp. nov., can be found in the Western Atlantic, which diverged from its sister species, Bathygobius antilliensis, around 3.03 Mya [cytochrome c oxidase I (COI) d = 0.063; cytochrome b (cyt b) d = 0.074]. There are several old mitochondrial lineages and limited gene flow among major biogeographic provinces of both B. soporator and B. geminatus (COI: overall ΦST = 0.32, P < 0.05; overall ΦST = 0.31, P < 0.05, respectively). We discuss how the Atlantic biogeographical barriers appear to have influenced the formation of the sister species of Bathygobius, and we formulate hypotheses on how the intermittent nature of biogeographical barriers, coupled with the ecological and biological traits of species and ecological and hydrological characteristics of the provinces, shaped the genetic structure and phylogeography of B. soporator and B. geminatus.