Phronimid amphipods are oceanic crustaceans associated with gelatinous zooplankters. Their host organisms belong mainly to two taxonomic groups: tunicates (salps or pyrosomes; subphylum Tunicata) and siphonophores (Cnidaria). After these amphipods devour the inner tissues of their hosts, they display the unique behavior of modifying their hosts into hollow barrel-shaped shelters, which are then utilized as neonatal nurseries by the females. Although previous studies have revealed the host specificity of these amphipods, it has not been inferred which types of hosts ancestral phronimids could have originally used. Moreover, morphological changes associated with host switching have not yet been studied. To deduce the evolutionary patterns of host switching, we investigated the phylogenetic relationships of phronimid species by using two genes: (1) cytochrome c oxidase subunit I (COI) and (2) 18S ribosomal RNA (18S). In addition, a morphometric analysis was conducted in order to better understand the morphological relationships between phronimids and their host organisms. Our phylogenetic analysis suggests that the ancestral host animals of phronimids could have been tunicates and that the host organisms have independently switched from tunicates to siphonophores at least twice in the family Phronimidae. Our morphometric analysis revealed that phronimids using siphonophores as hosts have a relatively shorter pereopod 5 compared to those using tunicates. The shortening of pereopod 5 seems to be an adaptation to the narrower internal space of siphonophore barrels compared to those of tunicates.