Recovery plans for many endangered fishes include production of large numbers of individuals in hatcheries to augment wild populations. However, effects of hatchery culture on phenotypic development are poorly documented for most species. June sucker (Chasmistes liorus) is an endangered lake sucker endemic to Utah Lake (Utah, USA), and recovery plans include raising thousands of juveniles to stock in the lake. To determine effects of hatchery culture on morphology of young June sucker, we raised individuals from four different families in both lake and hatchery environments and compared shape variation among families and between environments. We compared shape from three perspectives: lateral body, ventral mouth, and lateral head views. Mean shape varied between hatchery-reared and lake-reared individuals in each of the three views. In addition, hatchery-reared individuals exhibited higher variance in shape both within and among families compared with shape variance in lake-reared individuals. Hatchery-reared individuals exhibited divergent phenotypes compared with lake-reared individuals. These results suggest that exposure to the native environment during early life stages may be important for phenotypic development suitable to native habitats. Hatcheries should incorporate designs and practices to minimize divergent phenotypic development of individuals.