Resource polymorphism is a ubiquitous phenomenon in vertebrates and may represent a critical intermediate stage in speciation. Freshwater lakes in high-altitude areas represent a natural system for understanding resource polymorphism in fishes in diverse lacustrine environments and a few co-distributed species. We report resource polymorphism in a cyprinid fish, Schizopygopsis thermalis, in Lake Amdo Tsonak Co, a headwater lake in the upper Salween River system. Two morphs, planktivorous and benthivorous, were identified according to geometric morphological and traditional linear traits. The planktivorous morph exhibits a longer head and lower jaw, larger asymptotic standard length (L∞), lower growth rate (k) and higher growth performance index (φ) than the benthivorous morph. With respect to descriptive traits, the planktivorous morph possesses a terminal mouth and a highly developed mucus cavity in the cheek and chin, while the benthivorous morph is characterized by an inferiorly positioned mouth with a sharpened horny edge on the lower jaw. Our results indicate that distinct pelagic-benthic resources and low interspecific competition in the lake drove the initial differentiation of the two morphs and that partial spatial reproductive isolation might maintain and reinforce the differences between them.