Boreal and cool temperate forests are the major land cover of northern Eurasia and information about continental-scale genetic structure and past demographic history of forest species is important from an evolutionary perspective and has conservation implications. However, although many population genetics studies of forest tree species have been conducted in Europe or Eastern Asia, continental-scale genetic structure and past demographic history remain poorly known. Here, we focus on the birch genus Betula, which is commonly distributed in boreal and cool temperate forests, and examine 129 populations of 2 tetraploid and 4 diploid species collected from Iceland to Japan. All individuals were genotyped at 7 to 18 nuclear simple sequence repeats (nSSRs). Pairwise F’ST among the six species ranged from 0.285 to 0.903, and genetic differentiation among them was clear. STRUCTURE analysis suggested that Betula pubescens is an allotetraploid and one of the parental species was B. pendula. In both species pairs of B. pendula and B. plathyphylla, and B. pubescens and B. ermanii, genetic diversity was highest in central Siberia. A hybrid zone was detected around Lake Baikal for eastern and western species pairs regardless of ploidy level. Approximate Bayesian Computation (ABC) suggested that the divergence of B. pendula and B. platyphylla occurred around the beginning of the last ice age (36.300 years BP, 95%CI: 15.330 - 92.700) and hybridization between them was inferred to have occurred after the last glacial maximum (1.614 years BP, 95%CI: 561 - 4.710), with B. pendula providing a higher contribution to hybrids.