A comparative genomics approach determined that shared neuromolecular mechanisms could underlie behavioral response to territory intrusion across species spanning a broad phylogenetic range. A territory intrusion modulated similar brain functional processes in each species, including those associated with hormone-mediated signal transduction and neurodevelopment. Changes in chromosome organization and energy metabolism appear to be core, conserved responses to territory intrusion. Several homologous transcription factors that are typically associated with neural development were also modulated across all three species, suggesting that shared neuronal effects may involve transcriptional cascades of evolutionarily conserved genes. These results provide support for conserved genetic “toolkits” that are used in independent evolutions of the response to social challenge in diverse taxa.