The use of phylogeny with uneven or limited taxon sampling may bias our interpretation of organismal evolution, for instance, the origin(s) of the deep-sea animals. The Mollusca is the second most speciose phylum, in which the Gastropoda forms the largest group. However, the currently proposed hypotheses of gastropod phylogeny are mainly based on part of their taxonomic diversity, notably on the large-sized and shallow-water species. In this study, we aimed at correcting this bias by reconstructing the phylogeny with new mitogenomes of deep-sea gastropods including Anatoma sp., Bathysciadiidae sp., Bayerotrochus teramachii, Calliotropis micraulax, Coccocrater sp., Cocculina subcompressa, Lepetodrilus guaymasensis, Peltospira smaragdina, Perotrochus caledonicus, Pseudococculinidae sp., and Shinkailepas briandi. This dataset provided the first reports of the mitogenomes for the Cocculiniformia, three vetigastropod superfamilies: Pleurotomarioidea, Lepetelloidea, and Scissurelloidea, and the neritimorph family Phenacolepadidae. The addition of deep-sea representatives also allowed us to evaluate the evolution of habitat use in gastropods. Our results showed a strongly supported sister-group relationship between the deep-sea lineages Cocculiniformia and Neomphalina. Within the Vetigastropoda, the Pleurotomarioidea was revealed as the sister-group of the remaining vetigastropods. Although this Glade was presently restricted to the deep sea, fossil records showed that it has only recently invaded this habitat, thus suggesting that shallow waters was the ancestral habitat for the Vetigastropoda. The deep-sea Lepetelloidea and Lepetodriloidea formed a well-supported Glade, with the Scissurelloidea sister to it, suggesting an early transition from shallow water to deep sea in this lineage. In addition, the switch between different chemosynthetic habitats was also observed in deep-sea gastropod lineages, notably in Neomphalina and Lepetelloidea. In both cases, the biogenic substrates appeared as the putative ancestral habitat, confirming the previously proposed hypothesis of a wooden-step to deep-sea vents scenario of evolution of habitat use for these taxa.