Species with multimodal communication integrate information from social cues in different modalities into behavioral responses that are mediated by changes in gene expression in the brain. However, the neuromolecular basis of behavior remains poorly understood. Here, we use RNA-Seq to analyze brain transcriptome responses to either chemical or visual social signals in a territorial lizard with multimodal communication. Using an intruder challenge paradigm, we exposed 18 wild-caught, adult, male Sceloporus jarrovii to either male conspecific scents (femoral gland secretions), the species-specific push-up display (a programmed robotic model), or a control (an unscented pebble). We conducted differential expression analysis with the reference genome of a closely related species, S. undulatus. Despite the large inter-individual variation, we found significant differences in gene expression in the brain across signal modalities and the control. The most notable differences occurred between chemical and visual stimulus treatments, followed by the control vs. visual stimulus treatment. Altered expression profiles can explain aggression differences in the immediate behavioral response to conspecific signals from different modalities. Shared differentially expressed genes between visual- or chemical-stimulated males are involved in neural activity and neurodevelopment, and several other differentially expressed genes in stimulus-challenged males are involved in conserved signal-transduction pathways associated with the social stress response, aggression, and the response to territory intruders across vertebrates (e.g. NF-κB, MAPK).