The migration pattern of juvenile temperate seabass Lateolabrax japonicus in the stratified estuary of the Yura River was examined using carbon stable-isotope ratios (δ13C). δ13C values of mysids, which are the most important prey items for this species, were consistently enriched in the lower estuary and surf zone (LES), while depleted in the freshwater zone (FW). δ13C values of juveniles in LES were enriched, while those in FW were depleted, consistent with the δ13C difference in prey items. The results of δ13C showed that many juveniles migrated upstream from April to June and most of them stayed in FW until at least July. Juveniles that stayed in FW and LES for a relatively longer period (> c. 20 days) showed higher condition factors than those that stayed in FW for a short period (several days). This indicates that residence in FW enabled juveniles to achieve as good a body condition as residence in LES.