In the present study, we assessed small fishes as potential feed fishes with the lowest mercury levels. The mercury levels of four small pelagic fishes and a benthic fish from the Pacific Ocean and the Sea of Japan, i.e., spotted chub mackerel Scomber australasicus, chub mackerel Scomber japonicus, horse mackerel Trachurus trachurus, round scad Decapterus punctatus, and bastard halibut Paralichthys olivaceus, were determined. Total mercury levels in fish muscle were measured using a reduction vaporizing atomic absorption method. There were no significant correlations between body weight and mercury levels for these species. However, significant differences were observed in the mercury levels of these species between the two catch locations, with fish caught in the Pacific Ocean having higher mercury levels. This difference may be due to the Pacific Ring of Fire, a highly seismically and volcanically active zone, which is located in the Pacific Ocean. Preference for these fishes for use in aquaculture should refer to the area where they are caught in addition to the species.