Abstract:Picea koraiensis and Picea koraiensis var. nenjiangensis were used as the materials. The genetic differences in genomic level between Picea koraiensis and its variety were identified using RAPD and ISSR markers. The optimal reaction system and program of the markers were found through the orthogonal experimental design. Three RAPD primers OPN07,OPA17,S25 and one ISSR primer ISSR67 were screened out to make identification between Picea koraiensis and Picea koraiensis var. nenjiangensis, in which the specific bands were amplified in genomic DNA of Picea koraiensis var. nenjiangensis at 1 000, 950, 1 500 and 2 000 bp in molecular size, but not in Picea koraiensis. The results indicated that RAPD and ISSR marker could be used to differentiate these two spruces. In conclusion, two spruce species were identified in molecular level in this study. The results will provide basic information for systematical evolution, species identification, and interspecies crossing of spruce in the future.