Ariids or sea catfishes are one of the two otophysan fish families (out of 67 families in four orders) that inhabit primarily marine and brackish waters, although some ariid species occur strictly in fresh waters. The Ariidae includes over a 150 species and many are of primary importance for tropical fisheries. Their classification has remained in disarray and recent studies that have intended to elucidate relationships among ariids have mostly focused on taxa from restricted geographic areas and comprehensive phylogenies are lacking. Furthermore, few efforts have been made to hypothesize biogeographic scenarios and evolutionary trends among ariids. This study inferred molecular phylogenies (up to ∼4 kb) for ariids based on the most inclusive taxon sampling to date (123 species/entities). The results support the monophyly of the Ariidae (four anatomical and three molecular synapomorphies) and the sister-taxa relationship between ariids and the Malagasy family Anchariidae. The Ariidae is divided into two basal lineages. The Galeichthyinae, new subfamily, includes one genus and four species from southern Africa (three species) and southwestern South America (one species), representing a remarkable case of transoceanic disjunction. Molecular data provided fully-resolved and well-supported phylogenies for galeichthyines, indicating that the South American species is nested within the African clade. An earlier study attributed galeichthyines' disjunct distribution to vicariance promoted by the final separation of Africa and South America (∼105 mya). However, chronological estimations via molecular clocks show that the timing of intercontinental divergence was 15.4–2.5 mya, implying transoceanic dispersal or recent vicariance. The subfamily Ariinae includes the remaining taxa (∼97% of ariid diversity). The topologies support the monophyly of ariines but up to ten genera previously validated are incongruent with the molecular phylogenies. New World ariines were paraphyletic and Old World ariines were grouped into a well-supported clade further divided into subclades mostly restricted to major Gondwanan landmasses. The general area cladogram derived from the area cladograms of ariines and other fish groups is largely congruent with the geological area cladogram of Gondwana. Nonetheless, molecular clock analyses provided highly variable estimations on the timing of ariine diversification (∼28–105 mya). Habitat distributions (freshwater vs. marine) were optimized onto the phylogeny to test whether freshwater ariids are primitive (i.e., retain the ancestral freshwater otophysan condition) or derived (i.e., involve marine-to-freshwater transitions). The reconstructions support the latter scenario, suggesting a single invasion of marine waters at the root of the ariid tree followed by multiple events of freshwater recolonization in the Ariinae. Ariids provide an extraordinary example of bidirectional habitat transitions in fishes.