Uncovering how populations of a species differ genetically and ecologically is important for understanding evolutionary processes. We investigated genetic structure using nuclear microsatellites and chloroplast DNA sequences and geographical variation in leaf morphological traits among Magnolia salicifolia populations across its entire species range. Two distinct lineages, northern and southern lineages, were genetically detected and both lineages had substructure among populations. The width/length ratio and area of leaves showed latitudinal gradients, while the position of the maximum leaf width exhibited a discontinuous change between the lineages. Approximate Bayesian computation detected exponential population growth and stable population size from the past to the present in the northern and southern lineages, respectively. Small amounts of migrations between the lineages were inferred. Divergence time between the lineages was estimated to be the early to middle Pleistocene. Ecological niche modeling showed single large potential distribution area on the Sea of Japan side and multiple intermittent ones on the Pacific Ocean side during the last glacial maximum. We suggest that these distinct evolutionary histories of the northern and southern lineages after diversification have influenced not only neutral markers but also genes controlling leaf morphological traits.