A major challenge in biology is to understand how inherited variation results in phenotypic differences, especially for complex polygenic traits like behavior. Integrating genetic variants associated with evolutionary differences in honey bee aggression with genes identified via brain single-cell (sc) transcriptomics and sc gene regulatory network (GRN) modeling, we achieved robust genotype-to-phenotype mapping. We identified genetic differences in GRN structure associated with evolutionary differences in aggression, located in specific brain cell populations related to olfaction and vision. Some involve serotonin, which already was known to influence bee aggression, but not yet from a genetic perspective. These results demonstrate that, as theory predicts, GRN analysis can integrate evolutionary and systems biology to identify molecular mechanisms underlying adaptive polygenic traits.One Sentence SummaryGenetic variation affects behavioral variation by causing changes in brain cell gene regulatory networks.