The Chinese yew (Taxus wallichiana), which is widely distributed in the Himalayas and in southern China, is now on the edge of extinction. In order to understand the evolutionary processes that control the current diversity within this species at the genetic and ecological levels, its genetic patterns and range dynamics must first be identified and mapped. This knowledge can then be applied in the development of an effective conservation strategy. Based on molecular data obtained from 48 populations of T. wallichiana, we used GIS-based interpolation approach for the explicit visualization of patterns of genetic divergence and diversity, and a number of potential evolutionary hotspots have been specifically identified within the genetic landscape maps. Within the maps of genetic divergence and diversity, five areas of high inter-population genetic divergence and six areas of high intra-population genetic diversity have been highlighted in a number of separate mountain regions, and these evolutionary hotspots should have the priority to be protected. Furthermore, four geographical barriers have been identified: the eastern Himalayas, the Yunnan Plateau, the Hengduan Mountains and the Taiwan Strait. According to ecological niche modeling (ENM), the populations of T. wallichiana within the Sino-Himalayan Forest floristic subkingdom experienced westward expansion from the periods of Last Inter-glacial to Last Glacial Maximum (LGM). Following the LGM, the distribution range overall became reduced and fragmented. These findings challenge the classic mode of contraction-expansion in response to the last glaciation. In conclusion, our findings suggest that the changes in geographical landscapes and climate that occurred during the Quaternary resulted in current genetic landscape patterns.