Skylark Alauda arvensis japonica breeds in Hokkaido as a migrant and in other regions as a resident in Japan, and both of A. a. pekinensis and A. a. lonnbergi are considered winter visitors. The breeding habitats are open grassland at lowlands in general, however, small breeding populations were confirmed at alpine and subalpine habitats recently. To clarify the genetic structure of skylark population with regional and altitudinal differences, we analyzed mitochondrial DNA and nuclear DNA using samples from lowland and mountain populations of various regions in Japan, and also from the populations of Sakhalin and Primorye regions in Russia.

Japanese population formed a cluster different from Russian population in the phylogenic trees based on mitochondrial ND2 and Co1 gene sequence data, and these data also showed a clear genetic differentiation between the local populations in Kyushu and in other regions of Japan. The analysis with four markers of microsatellite revealed some differences in allelic frequencies between lowland and mountain sites, suggesting local populations in some mountain habitats may genetically differ from lowland populations.