Mt. Manokami, the Zao Mountains hasbeen defined as the northernmost natural distribution of Japanese larch (Larix kaempferi). The larch of Mt. Manokami is similar to Kurile larch (L. gmelinii var. japonica) in morphological and physiological characteristics rather than Japanese larch. This made quite a few researchers doubtful whether the larch was classified as Japanese larch recently. In this paper, DNA systematical study was carried out in order to reveal the phylogenetical relationship of this larch and to estimate its genetic diversity. The chloroplast genome and nuclear genome of Manokami larch were compared with Japanese larch in the Central Japan, Kurile larch and Korean larch (L. gmelinii var. olgensis). The rbcL gene sequence of Manokami larch was completely the same as Japanese larch, but it was different from the sequences of Kurile larch and Korean larch. This result made it clear that Manokami larch was closely related to Japanese larch phylogenetically. RAPD analysis of nuclear genome supported this result. The nuclear genome compositions between Manokami larch and Japanese larch, however, were different, and genetic differentiation was recognized. The genetic differentiation and morphological difference between them suggested that Manokami larch should be classified as a variety of L. kaempferi. Manokami larch that is small population size was poor of genetic diversity as a result of bottle neck effect.