Megalobrama pellegrini, a cyprinid endemic to the upper Yangtze River China, has thick keratinized beaks on the jaws and feeds on algae and molluscs. The size of keratinized beaks varies among different individuals. In the present study, two populations, from Longxihe (LXH) and Chishui (CSH) Rivers, were examined in order to explore the morphological variation of keratinized beaks, together with an analysis of intestine length and of stable isotopes. The results showed that the ratio of upper to lower keratinized beaks varied from 0.84 to 2.06. We defined the ratio < 1.25 as equal beak (EB) form, while >1.26 as thicker upper beak (TUB) form. In the LXH population, there were more TUB forms, while EB forms dominated in CSH population. Intestine length showed a negative relationship with the upper to lower beak ratio (Pearson correlation coefficient = -0.697, P < 0.01) indicating the possible adaptation of beak size to food type. In addition, analysis of stable isotope showed that these two populations differed in their food, and there was a positive relationship between trophic niche and size of beaks (R = 0.5530 and 0.4927, respectively). This further supported the suggestion that the beak size was possibly adapted to food type, with the TUB form to a higher trophic niche and the EB form to a lower trophic niche.