Species delimitation in the Abies chensiensis complex, consisting of A.chensiensis, A.recurvata, A.ernestii and A.ernestii var. salouenensis, has been the subject of a long-term dispute, as various taxonomic combinations have been proposed. We combined different lines of evidence, including morphological characters and mitochondrial and plastid DNA sequence data, to assess species delimitation. Plastid DNA sequence variation was highly consistent with the morphological result and separated A.recurvata from the other three taxa, but the mitochondrial DNA genealogy was more strongly related to geographical distribution rather than species delimitation, as proposed in previous studies. On the basis of morphological characters and plastid DNA sequence variation, the current species status of A.recurvata was well supported, and we also accepted A.ernestii and A.ernestii var. salouenensis as varieties of A.chensiensis. Furthermore, the phylogeographical history of A.chensiensis was surveyed by molecular data and ecological niche modelling. On the basis of molecular data, the current phylogeographical pattern of the A.chensiensis complex was probably shaped by recent rapid expansions from multiple refugia in the Hengduan Mountains and habitat contraction after the last glaciation. This hypothesis was supported by the results of ecological niche modelling and previous fossil records. Our findings suggest that these fir taxa might have continued to expand their range after the largest glaciation until the end of the last glaciation, but have contracted since then with the increasing temperature and habitat changes.