Mimura, M. 2013. Genetic and phenotypic variation in Lotus japonicus (Regel) K. Larsen, a model legume species. Can. J. Plant Sci. 93: 435–444. Lotus japonicus is a model legume species with more than 90% of its gene space determined; however, its ecological and evolutionary background is little known. The genetic and phenotypic variation of this model species was investigated within the Japanese Archipelago, where it exists in various climates and has experienced repeated vegetative shifts in conjunction with historical climate changes, using nuclear microsatellite loci and common garden experiments. The partial Mantel test was performed to detect the influence of phylogeographic effects on phenotypic variation among accessions along environmental gradients. Western Japan showed more complex genetic population structures than northern Japan, which may reflect past population dynamics. The total biomass demonstrated clinal variation with a climatic variable (ClimatePC). The trend was significant in a partial Mantel test when controlling for genetic distance, which is independent of the environmental distance. This suggests adaptive divergence within the Japanese Archipelago. With highly accessible genome information, L. japonicus appears to be a promising species for future ecological and evolutionary studies.