Little is known about the molecular, genetic, and physiological mechanisms that regulate phenotypic plasticity, while even less is known about how these mechanisms evolve. For selection to act upon phenotypic plasticity, there must first be genetic variation in a plastic response and the mechanisms that generate it. In this study, we measure the genetic variation in the thermoplasticity of abdominal pigmentation in female Drosophila melanogaster among 110 isogenic lineages from Drosophila Genetic Reference Panel (DGRP). We used a novel approach to quantify various aspects of dorsal pigmentation from digital images. Using these data, we characterize the genetic architecture of the thermoplasticity, correlating variation in the thermoplasticity of pigmentation with variation in the thermoplasticity of other morphological traits. In general, the thermal reaction norms for pigmentation were non-linear, and variation in the thermal plasticity of pigmentation among lineages was not correlated with variation in the thermal plasticity of body and organ size. Nevertheless, there was some overlap among the SNPs associated with the thermoplasticity of both pigmentation and size, suggesting some common mechanisms regulate the thermoplasticity of different traits.