Aggression is an evolutionarily conserved complex behavior essential for survival and the organization of social hierarchies. With the exception of genetic variants associated with bioamine signaling, which have been implicated in aggression in many species, the genetic basis of natural variation in aggression is largely unknown. Drosophila melanogaster is a favorable model system for exploring the genetic basis of natural variation in aggression. Here, we performed genome-wide association analyses using the inbred, sequenced lines of the Drosophila melanogaster Genetic Reference Panel (DGRP) and replicate advanced intercross populations derived from the most and least aggressive DGRP lines. We identified genes that have been previously implicated in aggressive behavior as well as many novel loci, including gustatory receptor 63a (Gr63a), which encodes a subunit of the receptor for CO 2 , and genes associated with development and function of the nervous system. Although genes from the two association analyses were largely nonoverlapping, they mapped onto a genetic interaction network inferred from an analysis of pairwise epistasis in the DGRP. We used mutations and RNAi knock-down alleles to functionally validate 79% of the candidate genes and 75% of the candidate epistatic interactions tested. Epistasis for aggressive behavior causes cryptic genetic variation in the DGRP that is revealed by changing allele frequencies in the outbred populations derived from extreme DGRP lines. This phenomenon may pertain to other fitness traits and species, with implications for evolution, applied breeding, and human genetics.Drosophila Genetic Reference Panel | genome-wide association mapping | extreme QTL mapping | advanced intercross population | epistasis A ggression is a near-universal animal behavior, important for securing food resources, defense against predators, gaining access to mating partners and, among social animals, creating and maintaining dominance hierarchies. Aggressive behavior is a typical quantitative trait, with natural variation attributable to segregating variants at multiple interacting loci, the effects of which are sensitive to the physical and social environments to which the individuals are exposed (1). Sociopathic and violent behaviors place a significant socioeconomic burden on human societies. However, disentangling the relative genetic and environmental contributions to aggressive behavior in natural populations is challenging due to its low heritability, and, in humans, because of the difficulty in accounting for social and other environmental influences, precisely quantifying aggression, and comorbidity with other psychological disorders.These challenges can be overcome using animal models. Numerous studies have highlighted the evolutionary conservation of neural pathways affecting aggression (2-4). Genes affecting bioamine signaling affect aggressive behavior in humans (4, 5), mice (6-8), and Drosophila (9-15). The nuclear receptor subfamily 2, group E, member 1 gene Nr2e1 affects aggressiv...