Sipunculans are non-segmented marine worms with an anterior retractable introvert, which are commonly included in Annelida based on molecular phylogenetic and phylogenomic analyses. They generally burrow in the soft sediments or live inside the crevices of hard substrata (e.g. calcareous/coralline rocks). However, members of some sipunculan genera (mainly Phascolion and Aspidosiphon) are known to have a peculiar habit of dwelling in vacant shells of gastropods or scaphopods. In this study, we investigated the shell utilization and preference pattern of the species of Phascolion and Aspidosiphon in Japan. We collected 302 sipunculans, comprising 273 and 29 individuals in Phascolion and Aspidosiphon, respectively, from 57–800 m depth of three study sites in the Pacific coast of Honshu Island, Japan. The species of Phascolion were found in vacant shells of 38 genera of 27 families of gastropods and six genera of four families of scaphopods, whereas the species of Aspidosiphon were found in 11 genera of 11 families of gastropods and one genus of scaphopod. These results suggest that members of each genus use a wide range of gastropod and scaphopod shells. The body size of the sipunculans was positively correlated with the shell size, suggesting that they change the shells as they grow. Furthermore, we investigated the shell preference of Phascolion species by comparing morphological characteristics of shells occupied and unoccupied by sipunculans. Generalized linear mixed model (GLMM) analyses suggest that the species of Phascolion tend to use long and narrow shells. Such shells likely fit well the elongated trunk of sipunculans.