<p><i>Micranthes nelsoniana</i> is called a species complex. Although many <i>M. nelsoniana</i> varieties with different morphologies are known, the boundaries of the varieties are unclear. In Kamchatka, particularly large morphological and ecological variations are observed. Studies on chromosome numbers in the North Kamchatka–Chukotka region suggest that polyploidy and genetic diversity may be involved in these variations. In this study, we investigated the background of these variations by examining allele combinations in the nrDNA rITS region and ploidy in populations of the Kamchatka Peninsula. The results showed that different allele groups, including circumpolar-continental and southern Kamchatka–Kuril Island types, are mixed throughout the Kamchatka Peninsula. In addition, tetraploids with various allele combinations and chromosome numbers were prevalent in the central part of the Kamchatka Peninsula. Our findings suggest that in central Kamchatka, diversification by allopolyploidy is promoted and the ease of chromosome number variation is involved in the combination of alleles.</p>