Abstract:The genetic diversity of 7 wild populations and 2 cultivated populations was analyzed using inter-simple sequence repeat(ISSR) markers. As a result,124 bands were amplified by 11 informative and reliable primers ,of which 110 were polymorphic loci. As analyzed by the software POPGENE,the genetic diversity of Chimonanthus praecox was high with Nei’s gene diversity of 0.272 6 and Shannon’s Information Index of 0.411 7. the genetic diversity difference among populations was high with PPL of 52.94%~90.00%,Nei’s gene diversity of 0.143 4~0.378 2 and Shannon’s Information Index of 0.232 2~0.546 6. Genetic differentiation mainly occurred within populations(GST=0.353 6). UPGMA cluster analysis based on Nei and Li genetic similarity didn’t form 9 clades corresponding to geographic distance. The correlation between genetic distance and geographic distance among the populations was not significant (r=0.437 1,P=0.921 3).