This study provides the first comprehensive chemical and molecular analysis of reproductive dominance in paper wasps. Cuticular hydrocarbon profiles and genome-wide patterns of brain gene expression were primarily associated with season/social environment rather than dominance status. In contrast, gene expression patterns in the ovaries were associated primarily with caste and ovary activation. Comparative analyses suggest that genes identified as differentially expressed in wasp brains are not related to queen pheromonal communication or caste in bees, but were significantly more likely to be associated with aggression in other insects (bees, flies), and even a mammal (mice). Genes involved in social regulation of reproduction in Polistes may have conserved functions associated with aggression in insects and other taxa.