Bayesian and maximum-likelihood phylogenies of Vetigastropoda (Mollusca: Gastropoda) were reconstructed by separate and combined analyses of one mitochondrial (cytochrome oxidase I, COI) and two nuclear (histone H3 and 18S rRNA) gene sequences, with an emphasis on dense taxonomic sampling. More than 70 vetigastropod species belonging to 13 families and 25 subfamilies constituted a robust clade against the two outgroup clades Neomphalina and Cocculinoidea. The phylogenetically controversial family Seguenziidae appeared as a derived Vetigastropoda and constituted a highly supported clade with eucycline and cataegine trochids, and three skeneimorphs (Adeuomphalus, Ventsia and Xyloskenea). These taxa herein treated as the superfamily Seguenzioidea are morphologically very diverse and grouped only by the combination of symplesiomorphies in the shell, radular and head-foot characters. Anatomical peculiarities of Seguenziidae, including the presence of the penis and seminal receptacle, are all apomorphic conditions independently derived from those in higher gastropod clades, as a consequence of the small size and in response to deep-sea habitats, where sperm storage seems to be especially beneficial with low numerical density of individuals and limited periodic cues for gametogenesis. Indeed, internal or semi-internal fertilization has been evolved at least six times in Vetigastropoda, essentially in deep-sea lineages, with weak phylogenetic constraints. Other new vetigastropod clades with high support values include: Turbinidae + Tegulinae (Trochidae) + Skeneidae s.s., Clypeosectidae + Lepetodrilidae, Anatominae (Scissurellidae) + Bathyxylophila (Skeneidae) and Lepetodriloidea + Scissurellidae +Bathyxylophila.