Two chloroplast DNA intergenic spacers, trnLtrnF and rpl16, were employed to study phylogeography of Saxifraga tangutica, which aimed to explore genetic structure and phylogeographical history of this species. The result showed that: (1) based on rangewide sampling (18 populations and 209 individuals), we detected 74 haplotypes. Only one haplotype (H5) was widespread, while 71.62% were private haplotypes, i.e., observed in single populations. (2) Analysis of molecular variance showed that withinpopulation variation was described as 91.85% of the total variation, while amongpopulation variation was not distinct (F_ST = 0.081). An estimation of nonsignificantly larger N_ST (0.109) than G_ST (0.097, P > 0.05) value across all populations suggested an absence of phylogeographical structure across the whole distribution range. (3) Neutrality tests of Tajimas D (-2.045 07, P < 0.05) and Fu & Li D^* (-3.629 27, P < 0.05) showed significantly negative values, in combination with unimodal of mismatch distribution analysis, suggested a recent demographic expansion of S. tangutica. Based on results given above, we speculated that there might be multi microrefugia for S. tangutica on the QinghaiTibetan Plateau platform during Quaternary glaciations. Climatic oscillations during Quaternary glaciations fragmented the distribution range of S. tangutica into isolated populations, subsequent allopatric divergence resulted in the formation of numerous private haplotypes across its distribution range. Populations of S. tangutica possibly experienced in situ altitudinal migrations to respond glacial and interglacial intervals, instead of extensively horizontal migration.