Fallen Rock Ptarmigan (Lagopus mutus) feathers from bird habitats were used to extract DNA and produced a clear PCR band after the second PCR with grouse-specific primers. Comparison with chicken and quail revealed that the mitochondrial control regions of the Rock Ptarmigan and Hazel Grouse (Bonasa bonasia) can be divided into three domains: a more conserved segment of the central domain with the F, D, and C boxes and CSB-1, as well as more variable regions of the left and right domains. Only two haplotypes were found in the Japanese Rock Ptarmigan at the 441 by of the left domain: haplotype LM1 in 21 samples from 4 localities in the Hida mountains and haplotype LM2 in 1 sample from the Akaishi mountains. The same region was analyzed using 36 individuals of Hazel Grouse from Hokkaido, which exhibited 21 substitutions defining 21 haplotypes, indicating that the Japanese Rock Ptarmigan area has very low genetic variability. Palynological study indicated Pinus pumila zone, where is main habitat of the Japanes Rock Ptarmigan, would have been scaled down during the early hypsithermal interval. Such a natural environmental change might cause a bottleneck event to the Rock Ptarmigan population, resulting very low genetic variability.