In Hiroshima Bay, parasitic isopods of the genus Mothocya infest the black sea bream Acanthopagrus schlegelii (Bleeker, 1854) and the Japanese halfbeak Hyporhamphus sajori (Temminck and Schlegel, 1846), two fish species that are abundant and commercially important in the Seto Inland Sea of Japan. Immature and mature Mothocya individuals can infect both juveniles and adults of H. sajori, while immature Mothocya are known to parasitize juveniles of A. schlegelii; i.e., no Mothocya parasites are found in adult A. schlegelii. The identification of the immature Mothocya parasitizing juveniles of A. schlegelii remains uncertain, because Mothocya species are morphologically identifiable only based on adult females. Also, the biological/ecological relationship between the hosts and parasites has not been studied. Here, we identified the parasites on A. schlegelii as Mothocya parvostisBruce, 1986 by molecular sequence analyses along with other parasites obtained from H. sajori, the latter being morphologically confirmed by comparison with paratype materials of M. parvostis as well as the similar congener Mothocya sajoriBruce, 1986. The growth rates of the infected A. schlegelii juveniles from June to September in the years 2013–2015 and 2018 were significantly lower than those of the uninfected ones, suggesting a negative effect of the infection on the hosts. Our data on the prevalence and duration of the infection, as well as the body size gain of the hosts and parasites, corroborate a hypothesis that M. parvostis would utilize A. schlegelii as an optional intermediate host before it reaches the final host, H. sajori.