Published and unpublished data are used to investigate possible mechanisms of species diversification in two key groups of Antarctic organisms: the Notothenioidei and the Euphausiidae. Species distributions are mapped onto molecular phylogenies, and this evidence is interpreted in light of the various ecological and historical factors which characterize the Southern Ocean. The joint effect of diverse agents (vicariance, “jump” dispersal) appears to be determinant in several cases for species divergence. A review of results from population genetics studies, together with new molecular evidence, confirm the importance of physical barriers (oceanographic fronts) in reducing migration, thereby promoting speciation, at least in notothenioids.