In this study we aimed to delimit the boundaries of the Sibbaldia procumbens species complex, integrating morphological, geographical and molecular data at the population level. In total, 246 individuals were tested with simple sequence repeat (SSR) markers, and individuals were classified into three clusters. Stable variation in the morphology of leaflets, episepal and achenes was found between individuals from eastern and western Tibet, and this corresponds to the observed genetic structure when K = 2. The combined analysis of morphology and SSRs suggests three species should be recognized in the complex in China (S. procumbens, S. cuneata and S. aphanopetala). The ranges of these three species are mostly geographically separate from each other. Sibbaldia aphanopetala has often been treated as a variety of S. procumbens, but here we restore it to species rank.