Abstract The fish stocking in captivity for later release into natural water bodies has historically been applied in Brazil, as a measure to mitigate impacts caused by dams. However, the released fish are adapted to the hatchery environment, which is totally different from the natural, which results in low post-release survival rates and ineffectiveness of stocking as a management measure. Worldwide, several studies have demonstrated the existence of large phenotypic differences between farmed and wild fish, but in Brazil, there is a great need for this kind of study. Based on this, our objective here was to verify if hatchery fish differ morphologically from its wild counterparties, at the same size class. Hence, a population of young Prochilodus lineatus raised in a fish farming station was compared with another from marginal lagoons of the Grande river. The results indicated that the fish farming resulted in morphologically different individuals of P. lineatus and a less diverse population, compared with wild fish. Measures such as environmental enrichment of hatchery tanks should be studied as a way to increase environmental heterogeneity and increase the morphological variability of the fingerlings produced.