Chloroplast DNA fragments (rbcL, trnSG) and nuclear ribosomal DNA internal transcribed spacer (ITS) were employed for studing population genetic diversity of Saxifraga atrata, which has a narrow distribution range endemic to the Qilian Mountains. The aim was to reveal genetic structure and population historical evolution of S. atrata. The results showed that: (1) four cpDNA and nine ITS haplotypes were isolated among the 115 individuals. Populations from the southeast edge of the Qilian Mountains showed high haplotype richness and uniqueness, whereas northwest populations only harbored a few widespread haplotypes and usually showed low levels of genetic diversity. (2) Analysis of molecular variance (AMOVA) based on both cpDNA and ITS datasets showed that most variations were from withinpopulations. (3) Neutrality tests based on cpDNA dataset exhibited negative values, but not significant. However, mismatch distribution analysis strongly supported a recent expansion of S. atrata. According to extant genetic structure, we speculated that S. atrata retreated to the southeastern refugia of the Qilian Mountains during the Quaternary. The northwest populations were the result of recolonization during interglacial or postglacial periods. Founder effect associated with recolonization should be responsible for haplotype impoverishment and low levels of genetic diversity of northwest populations. Bottleneck effect and genetic drift might be much severe in this narrow endemic species due to small population size and fragmentation, resulting in extremely low levels of total genetic diversity and average withinpopulation diversity compared with other Saxifraga species widespread in the QinghaiTibet Plateau and Himalayas.