To the present, genetic variation and differentiation in forest tree species in Japan has extensively been revealed by analysis of neutral genetic markers. However, there have not been so many studies on phenotypic variation and differentiation in forest tree species since long ago. Magnolia kobus is a broad-leaved deciduous tree distributed from Kyushu to Hokkaido, Japan. M. kobus distributed in Hokkaido and the Sea of Japan side of northern and central Honshu has been taxonomically treated as a variety borealis, which is reported to have larger leaves and petals. The aim of this study is to evaluate intraspecific variation of M. kobus by using microsatellite markers and leaf morphology to judge whether the variety borealis can be recognized. Fresh leaves were collected from 16 populations throughout northeastern Japan. We used 295 trees for genetic analysis and 309 trees for morphological analysis. Morphological analysis revealed that the leaf areas of populations in Hokkaido and along the Sea of Japan side of Honshu were larger than those of Kanto district located on the Pacific side of Honshu. This result agreed with the taxonomic classification. However, we could not recognize the variety borealis genetically because the geographic pattern of genetic variation did not coincide with that of morphological variation.