Temperature is known to alter physiology and behavior in fish, but also has potential to alter morphology by impacting development and growth. In 2010, a population of Amargosa pupfish (Cyprinodon nevadensis amargosae) from a groundwater fed spring named Tecopa Bore in the Death Valley region of California, USA, experienced a mean temperature elevation of approximately 9°C following an anthropogenic alteration to its habitat. That temperature increase was accompanied by a 36% reduction in mean mass, 7.6% reduction in body length, and the partial or complete inhibition of paired pelvic fin development in 34% of the population. To further evaluate how higher temperatures influence morphology in pupfish, we compared body shape variation of Amargosa pupfish collected in 2013-2017 from Tecopa Bore to a conspecific allopatric population from the nearby, variable temperature Amargosa River. Pupfish in Tecopa Bore were again smaller, showed a reduced incident of pelvic fins, and also exhibited a proportionally larger eye and head. That combination of characteristics mirrors previously observed outcomes of plastic phenotypic responses of C. n. amargosae to high temperature in laboratory studies, suggesting that morphology of pupfish in Tecopa Bore may have emerged in part from developmental plasticity. Pupfish from Tecopa Bore also exhibited reduced sexual dimorphism in body depth compared to the river population, suggesting high temperature may also affect sex differences in shape. These observations implicate temperature variation having contributed to morphological divergence between the Tecopa Bore and Amargosa River populations, and point to the importance of considering how warming temperatures may affect morphology in other fishes.