Compared with traditional genetic markers, genomic approaches have proved valuable to the conservation of endangered species. Paeonia ludlowii having rarely and pure yellow flowers, is one of the world's most famous tree peonies. However, only several wild populations remain in the Yarlung Zangbo Valley (Nyingchi and Shannan regions, Xizang) in China due to increasing anthropogenic impact on the natural habitats. We used genome-wide single nucleotide polymorphisms to elucidate the spatial pattern of genetic variation, population structure and demographic history of P. ludlowii from the fragmented region comprising the entire range of this species, aiming to provide a basis for conserving the genetic resources of this species. Unlike genetic uniformity among populations revealed in previous studies, we found low but varied levels of intra-population genetic diversity, in which lower genetic diversity was detected in the population in Shannan region compared to those in Nyingzhi region. These spatial patterns may be likely associated with different population sizes caused by micro-environment differences in these two regions. Additionally, low genetic differentiation among populations (Fst = 0.0037) were detected at the species level. This line of evidence, combined with the result of significant genetic differentiation between the two closest populations and lack of isolation by distance, suggested that shared ancestry among now remnant populations rather than contemporary genetic connectivity resulted in subtle population structure. Demographic inference suggested that P. ludlowii probably experienced a temporal history of sharp population decline during the period of Last Glacial Maximum, and a subsequent bottleneck event resulting from prehistoric human activities on the Qinghai-Tibet Plateau. All these events, together with current habitat fragment and excavation might contribute to the endangered status of P. ludlowii. Our study improved the genetic characterization of the endangered tree peony (P. ludlowii) in China, and these genetic inferences should be considered when making different in situ and ex situ conservation actions for P. ludlowii in this evolutionary hotspot region.