ABSTRACT: Latitudinal clines of phenotypic traits have been repeatedly reported in various species. The present study, however, is the first to demonstrate that intra-specific latitudinal clines in body size can be reversed in geographically distinct areas. Life-history traits in the early ontogenetic stage of the amphidromous fish ayu Plecoglossus altivelis altivelis were compared across 2 sides of the Japanese Archipelago. We analyzed otoliths from 231 individuals collected from 23 rivers (11 and 12 rivers flowing into the Sea of Japan and Pacific Ocean, respectively) to determine age at upstream migration and growth rate. As widely observed across ectotherms, fish from higher latitudes displayed relatively slow growth. Slopes of these clines, however, differed between the 2 water bodies, resulting in counter-directional latitudinal clines of size at upstream migration. A positive latitudinal cline in body size in populations and negative latitudinal gradient in seawater temperature from the Pacific side was consistent with the temperature-size rule. In contrast, a negative latitudinal cline of migration size was found in the Sea of Japan. This arose partly from unexpectedly fast growth of fish in the southern Sea of Japan, likely achieved by local migration into more suitable thermal microhabitats during overwintering. Our findings highlight how phylogenetically prevailing patterns at the macrogeographic scale can be masked by mechanisms specific to particular taxa, such as life-history responses to thermal heterogeneities on a smaller scale.