Two species of Mothocya have previously been recorded from Hyporhamphus sajori: M. parvostis Bruce, 1986 and M. sajori Bruce, 1986. Mothocya parvostis is re-described based on the ovigerous female type and additional materials collected from the host from in and around the type locality. Morphological re-examination of fresh specimens and the type materials together with genetic data show that the M. sajori and M. parvostis are the same species, differing primarily in size, therefore we have placed Mothocya sajori Bruce, 1986 into a junior synonym of Mothocya parvostis Bruce, 1986. Mothocya parvostis is characterized by the following combinations of characters: 1) body slightly to moderately twisted to one side; 2) pereonite 7 posterior margin moderately to deeply recessed; 3) uropodal rami extending to pleotelson posterior margin; and 4) uropod rami bluntly rounded, exopod 1.5 times as long as peduncle. The differences of four morphological features for M. parvostis and M. sajori was quantified. Furthermore, a total of 635 isopods infesting H. sajori were collected from all over Japan to conduct quantitative morphological and molecular sequence analyses (mitochondrial cytochrome c oxidase subunit I and 16S rRNA). Although the four quantitative features did not overlap between the two species in type specimens, all quantitative morphological values of newly collected specimens in this study did not display a bimodal distribution. In addition, our molecular analyses found only a single clade for our newly collected specimens in neighbor-joining tree.