Organisms acclimate and adapt to complex environments in which multiple abiotic stressors may interact with genetic variation to determine the degree of stress experienced by individuals. The fruit fly Drosophila melanogaster encounters ethanol during development and shows latitudinal patterns of ethanol tolerance. The expansion of D. melanogaster into temperate latitudes that experience cooler and more variable environments is coincident with the evolution of a much higher ethanol tolerance that is considered to be adaptive. We characterized variation in whole-transcriptome responses of multiple D. melanogaster wild-type genetic strains from temperate latitudes to larval ethanol exposure (0 or 6%) at two temperatures (16 C and 25 C) by RNA-sequencing. We identified genes that exhibited genotype-by-environment (GxE), ExE and GxExE interactions. We found that diverse pathways and co-regulated networks of genes including lipid and phospholipid metabolism, drug metabolism, autophagy, and mitochondrial function responded to developmental ethanol and temperature exposure, and that some of the transcriptional responses were via the indirect effects of ethanol to delay development and generate cellular stress in certain genetic strains. Ethanol exposure appeared to cause oxidative stress through dysregulation of fatty acid metabolism, increased production of free radicals, and downregulation of scavengers of reactive oxygen species. Finally, we will synthesize these data on gene-expression plasticity with the plasticity that we have observed in the developmental and ethanol tolerance phenotypes of D. melanogaster larvae under the same environmental conditions.