Significance Mitigating thermal stress through evolutionary adaptation or physiological plasticity is critical for species’ persistence in changing climates. Sparse knowledge of genetic and physiological architectures of thermal plasticity hampers our ability to predict organismal resilience to climate change. Understanding the independence of short- and long-term plasticity and constraints of basal thermotolerance on plasticity is important for understanding responses to climate change. We show heritable genetic variation for basal cold tolerance and plasticity in a midlatitude Drosophila melanogaster population. High long-term plasticity predicted high short-term plasticity, and basal cold tolerance constrained both plasticity measures. There was no overlap in SNPs associated with either plasticity type. Overlapping molecular function of SNPs suggests shared physiology between long- and short-term plasticity, despite distinct genetic architectures.