The genus Brachymystax mainly distributes in the Amur River and streams of the Qinling Mountains of northern China. There is a debate on the validation of subspecies B. lenok tsinlingensis Li for a long time. Some ichthyologists thought that there should be two species (B. lenok and B. tumensis) in Amur River and a subspecies (B. lenok tsinlingensis) in the Qinling Mountains, while others believed no division of the subspecies. Thus, 169 specimens of Brachymystax spp. were collected from three locations (Heihe River, Amur and Ussuri River) to identify the taxonomic status in terms of morphological variation among these species or subspecies. Results of geometric morphometric analysis indicated significantly morphological variation in body shape among three morphotypes based on 18 landmarks. Principal component analysis (PCA) showed that the cumulative contribution rate of the first five principal components were 72.99%. CV1 (65.77%) and CV2 (34.23%) were well explained 100% of the observed variation among three morphotypes by Canonical variate analyses (CVA). The morphological variation was well defined by PCA and CVA: B. lenok tsinlingensis had wider and elongate head, the longest eye diameter and the widest dorsoventral orientation; B. lenok had tapered and narrow head, sharp snout and medium diameter of eye; B. tumensis had short head, blunt snout and shortest eye diameter and narrow dorsoventral orientation. Furthermore, discriminant function analysis (DFA) showed that all samples (except six) were correctly reclassified. Our morphological analysis supported the validity of taxonomic status of B. lenok and B. tumensis as two species, and B. lenok tsinlingensis could be considered as an independent species.