Sea hare species within the Aplysia clade are distributed worldwide. Their phylogenetic and biogeographic relationships are, however, still poorly known. New molecular evidence is presented from a portion of the mitochondrial cytochrome oxidase c subunit 1 gene (cox1) that improves our understanding of the phylogeny of the group. Based on these data, a preliminary discussion of the present distribution of sea hares in a biogeographic context is put forward. Our findings are consistent with only some aspects of the current taxonomy, and nomenclatural changes are proposed. The first is the use of a rank free classification for the different Aplysia clades and subclades as opposed to previously used genus and subgenus affiliations. The second is the suggestion that Aplysia brasiliana Rang, 1828 is a junior synonym of Aplysia fasciata Poiret, 1789. The third is the elimination of Neaplysia since its only member is confirmed to be part of the large Varria clade.