The aim of this study was to investigate the structure and ultrastructure of the digestive tract of Qinling lenok (Brachymystax tsinlingensis Li, 1966), a cold water Salmonidae fish, an endangered teleost species, with high potential for controlled rearing in Shaanxi Province of China, by light and electron microscopy. Morphological data of the digestive tract are important for understanding fish nutrition, pathological or physiological alterations. The histological structure of Qinling lenok consists of four layers: mucosa, submucosa, muscularis and serosa. Taste buds were found in lips and esophagus. The esophageal mucosa consists of undifferentiated mucous cells and surface epithelial cells. The U-shaped stomach was divided into cardiac, fundic and pyloric region. There are numerous gastric glands in the submucosa layer of the cardiac and fundic stomach, but none of them are present in the pyloric region. The convoluted tube-shape intestine is lined by simple columnar epithelial cells with microvilli at the apical surface, with an intestinal coefficient of 0.61. There are numerous goblet cells in the intestine. Finger-like pyloric caeca were found in the front of intestine tube, with number ranged from 42 to 88. In ultrastructural level, mucous and glandular cells in the stomach were found, the glandular cell with well-developed tubulovesicular system, a great amount of pepsinogen granules, mitochondria and Golgi apparatus. The enterocytes with abundant microvilli contained mitochondria and lysosome, and mucous granules of goblet cells were apparent in the intestine. High density of lipid droplets of pyloric caeca might be concerned with fat-absorption. The present study suggests that the digestive tract of Qinling lenok is similar to other carnivorous fishes, in relation to its feeding habits.