Abstract:This study used ISSR molecular marker technology to identify Larix gmelinii, Larix olgensis, Larix kaempferi and different clones. Thirteen ISSR primers which screened from fortynine primers can identify among larch species and clones,and the rate of the samples with specific band is 100%, this technology offers new ways and means for accurate identification of new larch species and elite seeds: there are five primers by which L. kaempferi, L. olgensis and L. kaempferi were amplified particularly, specific bands were produced at different location, as a species identification standards, nine primers can be amplified specific fragment in different kinds of larch clones respectively. It can identify the clones.