| Clintonia udensis Trautv. et Mey., a pennial herb, was belonged to Polygonateae (Liliaceae). There are two ploids (diploids and tetraploids) in this species, and the distribution of the tetraploids was narrow, and beseted in the diploids. The origin and differentiation of polyploidy were therefore important in speciation of this species. In the study, the genetic diversity and genetic differentiation were analysed by chloroplast microsatellite markers (cpSSR), then the division between the diploidy and tetraploidy was investigated, and these informations were used to probe into the polyploidy origin, dispersal and evolution of C.udensis.In this study, 19 populations, included 5 tetraploid populations, were analyzed to reveal the genetic diversity by using cpSSR markers. The results showed that 7 out of 11 pairs primers had various amplified productions, The proportion of polymorphic loci (PPB) was 63.64%, the average of polymorphic information content (PIC) was 0.2925. The genetic variations within population were detected only in two populations (BSLZ and ZKQ). The effective number of alleles per locus was only 1.4978. Net's gene diversity index (He) was 0.2633, and Shannon diversity index (I) was 0.3891, which indicated that the genetic diversity of C.udensis was median. Shannon index (Hst = 0.9928), Net's index (Gst = 0.9944) and the gene differentiation coefficient (Φst = 0.9932) together revealed that the molecular variation mainly existed among populations. This maybe caused by the change of reproduction strategy and the limited of gene flow among populations.The indices of genetic diversity in the tetraploidy were lower than that of the diploidy by software POPGEN32, and the analysis of genetic differentiation using AMOVE showed that there are 21.56% of genetic variations among the tetraploidy and the diploidy, which implied that the tetraploids had some genetic division with the diploid. But the tetraploids could not be grouped in one cluster, and had closed relationship with adjoined diploid by UPGMA analysis, and the same situation appeared in NJ tree of haplotype. The unique type of megasporogenesis maybe result in massive seed abortion in diploidy and tetraploidy hybridization, which limited the chloroplast gene introgression between different ploidy types of the species, and then result in the genetic division among different cytotype.Based on the analysis of haplotype, there are some conclusions: the tetraploidy had origined at least three times independent. One ocurred near Japan, and the others lay in China, contained Qin-Ba mountain system and Hengduan mountains. Origin of population in Tibet was not testified in this study.
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