Sea hares within the genus Aplysia are important neurobiological model organisms, and as studies based on different Aplysia species appear in the literature, a phylogenetic framework has become essential. We present a phylogenetic hypothesis for this genus, based on portions of two mitochondrial genes (12S and 16S). In addition, we reconstruct the evolution of several behavioral characters of interest to neurobiologists in order to illustrate the potential benefits of a phylogeny for the genus Aplysia. These benefits include the determination of ancestral traits, the direction and timing of evolution of characters, prediction of the distribution of traits, and identification of cases of independent acquisition of traits within lineages. This last benefit may prove especially useful in understanding the linkage between behaviors and their underlying neurological basis.