Abstract: Most Balitoridae fish with similar shapes separately distribute in different rivers or different sections of a river. Providing the morphological similarities, it’s interesting to find why Sinogastromyzon sichangensisandMetahomaloptera omeiensis coexist in the Zaodu River. To address this, the digestive systems of these two fish species were comparatively analyzed by morphological, histological and histochemical methods. The digestive systems of these two fish were nearly the same at morphology, which were consistent with characteristics of omnivorous fishes, however, the morphological difference of the digestive system was obvious. First, the intestine of S. sichangensis was circled into a" φ”shape, with hepatopancrease covered on the ventral part, however, that of M. omeiensis was organized in a complicated ways. Second, the gut index (GI) and digestive system index (DSI) of S. sichangensis were greater than those of M. omeiensis.Besides, the digestive tract of S. sichangensis had a significant higher mucosal fold and thicker muscular layer compared with M.oneiensis, however, there was no significant difference in hepatopancrease. The mucous secreting cells were similar in these two fishes based on AB (Alcian Blue) and PAS (Periodic Acid Schiff) staining, and most of these cells belong to type Ⅱ and Ⅳ mucous cells that were similar to most teleosts. The characteristics of digestive system reflect the feeding habits and digestive ability of fish, in some degree. Thus, the morphological and histological differences in digestive system between S. sichangensis and M. omeiensis may suggest different diet and digestion, which maybe the reasons for the coexistence of these two morphologically similar species.