Ngangtse Co (4535 m a.s.I., 840 km(2)) is a typical endorheic lake in Tibet. In 2015, we investigated the fish resource in this lake and its rivers and collected two Triplophysa species, including T. brevicauda and T. stewarti. To understand the evolutionary dynamics of Triplophysa in Ngangtse Co, the adaptive and genetic divergence between river and lake populations were investigated by analysing their morphological characteristics and mitochondrial COI and Cytb sequences. Among all of 277 samples, the ratios of the number of T. brevicauda to T. stewarti were 27:8, 34:11, 14:24, 37:0, 16:23 and 0:83 in river populations R-A, R-B, R-C, R-D, lakeside population LSE and lake population L, respectively. For T. brevicauda, a small but significant genetic divergence (mean F-ST = 0.0890) was detected between population R-D and other three river populations, and significant morphological differences of body length/body height and body length/caudal peduncle length were observed between population R-D and R-A, R-8, suggesting an association between differentiation and geographical distance. For T. stewarti, very high levels of genetic differentiation was observed between population L and other populations with the F-ST values ranging from 0.4737 (L-R-A) to 0.7074 (L-R-c). In addition, significant differences of most of morphological characteristics were observed between the lake (L) and river (R-C) populations, indicating that lake fish of T. stewarti was a population that showed a long-term adaptation to the saltwater lake. These results provide insights on the evolutionary dynamics of Triplophysa in Ngangtse Co and help us to understand the fish speciation in endorheic lakes on the Qinghai-Tibetan Plateau.