Tergipedidae represents a diverse and successful group of aeolid nudibranchs, with approximately 200 species distributed throughout most marine ecosystems and spanning all biogeographical regions of the oceans. However, the systematics of this family remains poorly understood since no modern phylogenetic study has been undertaken to support any of the proposed classifications. The present study is the first molecular phylogeny of Tergipedidae based on partial sequences of two mitochondrial (COI and 16S) genes and one nuclear gene (H3). Maximum likelihood, maximum parsimony and Bayesian analysis were conducted in order to elucidate the systematics of this family. Our results do not recover the traditional Tergipedidae as monophyletic, since it belongs to a larger clade that includes the families Eubranchidae, Fionidae and Calmidae. This newly recovered clade is here referred to as Fionidae, the oldest name for this taxon. In addition, the present molecular phylogeny does not recover the traditional systematic relationships at a generic level, and therefore, systematic changes are required. We recognize the following clades within Fionidae: Calma, Cuthona, Cuthonella, Eubranchus, Fiona, Murmania, Tenellia, Tergipes, Tergiposacca gen. nov., Rubramoena gen. nov. and Abronica gen. nov. The type species of Tergiposacca, T. longicerata nov. sp. is described. The other two new genera have a previously described species as their type species. Most of these taxa, with the exceptions of Eubranchus, Tergipes and Fiona are composed of radically different constituent species from their traditional membership, but appear to be supported by morphological synapomorphies as well as molecular data. Aenigmastyletus, Catriona, Phestilla, Tenellia and Trinchesia are nested within other clades and, thus are here considered as synonyms of the larger clades. The phylogenetic position and validity of Myja, Guyvalvoria, Leostyletus and Subcuthona still need to be tested in future studies when material becomes available.