Previous phylogeographical studies of the Sino-Himalaya (SH) regions have mainly focused on seed plants from forest or alpine grassland habitats, whereas the flora of the subnival summits, especially the ferns, has largely been ignored. Here, we report on phylogeographical studies on Polystichum glaciale, a rare fern endemic to the subnival belt of the SH region. Based on cpDNA/nDNA sequences, strikingly rich genetic diversity was detected in P. glaciale. Combined with the lack of 'isolation by distance' and the major genetic differentiation among populations revealed by AMOVA, they collectively suggested that P. glaciale exhibited island-like population genetic structure. Phylogeographical structure with two genetic groups (N vs. S) was further identified in P. glaciale by the SAMOVA based on cpDNA data, of which the geographical pattern was mainly associated with the biogeographical boundary between the northern and southern Hengduan Mountains at 29A degrees N latitude. We concluded that extremely complex topography of SH region and highly fragmented subnival habitat have played a critical role in shaping phylogeographical structure and genetic differentiation of P. glaciale. Mismatch distribution analyses and ecological niche modelling suggested P. glaciale has undergone north-westward retreat after the LGM. Predictions of its future distribution indicated the possibility of compression within suitable subnival habitats. We suggest in situ conservation should be urgently implemented to preserve this rare fern. Our results represent a first framework for a comprehensive understanding of the biogeographical history of fern species associated with the subnival belt of the SH region and the effects of historical events on its genetic architecture.