Quercus crispula var. horikawae is a shrub-type oak restricted on steep mountain slopes in heavy snow regions of Japan. It is recognized as a variety of Q. crispula. It has usually smaller leaves and denser hairs on abaxial leaf surface than Q. crispula. They are are classified as two distinct taxa but their genetic relationship remains unclear. We assessed the genetic structure of populations of the two taxa in order to clarify their genetic relationship. We collected samples from paired populations in each locality (19 populations in 9 localities, n = 575) and 5 independent natural populations of Q. crispula as reference and genotyped at 32 nuclear microsatellite loci. Genetic differentiation between taxa was low (F_ST = 0.056), but results of Principal Coordinate Analysis, model-based Bayesian clustering, and phylogenetic analyses agreed on genetic diversification of the two taxa, including detection of ecotypes. However, the two taxa formed as one genetic cluster when a closely related species Q. serrata was included in separate similar analyses, confirming that Q. crispula var. horikawae is a subset of Q. crispula.