Faced with rising environmental temperatures, there is growing evidence that species are exhibiting shifts in ecological distribution, physiological performance, and behavioral strategy. Less is understood, however, about links between environmental conditions and the precision with which organisms are able to fulfill their developmentally programmed phenotype. Here, we report that developmental instability, assessed by the fluctuating asymmetry (FA) of right versus left valves in intertidal mussel shells, increases under elevated thermal stress. In a growth experiment, mussels that were exposed to elevated aerial temperatures (21.5° ± 0.1°C) for three hours each day displayed higher levels of FA compared to mussels exposed to cooler aerial temperatures (12.6° ± 0.1°C). Reciprocal field transplant experiments revealed that FA increased under higher aerial temperatures (e.g., on a south facing surface [19.6° ± 0.2°C]) compared to individuals living in cooler habitats (e.g., on a north facing surface [15.2° ± 0.2°C] or lower in the intertidal zone [14.1° ± 0.6°C]). Together, these results imply that the precision of developmental processes can be perturbed by environmental conditions and raise developmental instability as a potential impact of future environmental variability alongside shifts in physiology, behavior and biogeographic distribution.