June sucker, Chasmistes liorus, is an endangered lake sucker endemic to Utah Lake, Utah, USA. Over the last two decades, captive-raised June suckers have been stocked into Utah Lake to augment the wild population. However, it has become apparent that the fish stocked from captive stock may not always represent the typical June sucker morphology. To determine the utility of current captive brood lots to produce June sucker phenotypes, we characterized shape of the lip lobes on the lower jaw of each brood lot. We obtained offspring from within-lot crosses and characterized shape of the lower lips using geometric morphometrics. We compared shape of brood lots to reference samples of June sucker and reference samples of the co-occurring sister species, Utah sucker (Catostomus ardens). Mean shape of the lower lips among brood lots varies from typical June sucker morphology to shapes typical of Utah sucker. Three brood lots had mean shape scores somewhat similar to the reference June sucker mean, and five brood lots had mean shape scores more similar to the reference Utah sucker mean. All other brood lots were intermediate representing hybrid phenotypes. Utilization of all brood lots on a roughly equal basis for augmentation in Utah Lake will likely result in the loss of typical June sucker morphology in the lake within a few decades. We recommend use of brood lots that exhibit June sucker morphology and discontinuance of use of brood lots that represent Utah sucker morphology. In addition, selection on lower lip shape in captive brood lots may be required to recreate June sucker phenotypes from captive brood stock.