Climate change and range shift during glacial cycles in the Quaternary resulted in disjunct plant distributions. Geographic genetic structure can imply historical processes that formed disjunct distributions. Betula dahurica Pallas is common in continental northeast Asia but is disjunctly distributed in the Japanese archipelago. To explore the formation process of its disjunct distributions, genome-wide single nucleotide polymorphism (SNP) genotypes, chloroplast (cp) DNA sequences, and leaf morphology were investigated in 10 populations in three regions, Primorsky, Hokkaido, and Honshu. Frequency distributions of the ratio of SNP reads suggested that most individuals in the three regions were octaploid, except for some hexaploid or heptaploid individuals found in Hokkaido and Honshu. SNP genotypes of putative octaploid individuals indicated that Honshu populations were diverged from Primorsky and Hokkaido populations. This genetic divergence was relatively small (0.010 < FST < 0.035) but larger than those between Primorsky and Hokkaido (FST < 0.010) and within regions (FST < 0.008). The effective population size in Honshu was smaller than that in Primorsky and Hokkaido. CpDNA (trnL–trnF) sequences found in Honshu were different from those found in Primorsky and Hokkaido. The variations in leaf size and shape were overlapped among the ploidy levels and among the populations. The findings of geographic genetic structure suggest a plausible process that formed the disjunct distributions, which includes the isolation of persistent populations in Honshu and the post-glacial migration from continental northeast Asia to Hokkaido directly or through Sakhalin.