Incorporation of deep-sea and small-sized species provides new insights into gastropods phylogeny.

•11 mitogenomes from the deep-sea gastropods were newly reconstructed.•First report of the mitogenomes for the Cocculiniformia.•Pleurotomarioidea is sister to the remaining vetigastropods.•Shallow water habitat is suggested to be the ancestral for the Vetigastropoda.•Deep-sea taxa from biogenic substrate and vent/seep are sister groups.