Otoliths grow throughout a fish’s life and are important for identifying fish stocks and fish age. This study aims to differentiate different stocks of Schizothorax grahami (Regan, 1904) in the Chishui River, an upper reach of the Yangtze River, by otolith morphology. The otolith morphology of S. grahami from three different river sections was analyzed using the Shape Index, Fourier coefficients, and wavelet coefficients. The composite discrimination success rate of the Shape Index was 59.7%, and it was difficult to distinguish in the scatter plots. In contrast, canonical principal coordinate scatter plots clearly showed three distinguished stocks. The above results indicate that otolith morphology can discriminate between stocks in plateau endemic fish, and several S. grahami stocks may be separately managed in the Chishui River.