Shallow-water marine invertebrates living near the upper limits of their thermal tolerances are uniquely susceptible to climate warming. This is particularly the case for species that occur in geographic regions where larval dispersal or adult migration to cooler waters is not an option. This scenario aptly describes populations of the seagrass-associated sea urchin Lytechinus variegatus inhabiting the northern Gulf of Mexico where northward movement is restricted by a coastline. In the present study, we exposed juvenile L. variegatus to chronic ambient (26 °C) and predicted near-future (30 °C) temperature treatments for 90 days. X-ray Diffraction (XRD) was employed to determine the Mg/Ca ratios of the spines, test, and Aristotle's lantern of individuals sub-sampled at 30, 60, and 90 days. We found that while individuals grew at similar rates, Mg/Ca ratios in all skeletal components were overall significantly lower in individuals held at 30 °C than at 26 °C.