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Abstract: In this paper, we report the phylogeographic history of Clintonia udensis Trautv. & Mey. (Liliaceae) inferred from two types of chloroplast DNA markers, polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and DNA sequences. Eighty samples were collected from 20 natural populations, 19 located in China and one in Japan, across the entire range of the species in East Asia. High genetic diversity (h T(PCR-RFLP)=0.972, h T(sequencing)=0.874) and significant differentiation (N ST(PCR-RFLP)=0.893, N ST(sequencing)=0.988 and G ST(PCR-RFLP)=0.777, G ST(sequencing)=0.978) were detected at the species level. These findings are consistent with a scenario of clonal reproduction and locally restricted gene exchange. The level of diversity of tetraploid populations was slightly greater than that of diploid populations. Significant molecular variation was found between tetraploids and diploids. Tetraploids may be autopolyploids and may have formed repeatedly in different locations. At least three regions of origin could be recognized. Twenty-six distinct haplotypes were identified. Haplotype frequency distributions were strongly skewed, with most haplotypes (n =25) represented by only one sample each and thus restricted to a single population. Non-overlapping distributions of cpDNA haplotypes and strong genetic differentiation among populations and/or different ploid level were consistent with the findings of a nested clade analysis, which inferred long-distance colonization as the major process influencing the spatial haplotype distribution of this species. Nested clade analysis showed that the 26 haplotypes formed two 3-step, four 2-step and eleven 1-step clades, with twelve clades showing significant geographical associations. Higher N ST than G ST (P <0.05) suggested a distinct phylogeographical pattern. Based on mismatch distribution analysis and neutrality tests, we found no evidence of population expansion in the species. Our analyses indicate that the history of C. udensis involved both long-distance migration and the tectonic events of Mountains in East Asia. [Copyright &y& Elsevier]