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Abstract Gene co-expression networks are a widely used tool for summarizing transcriptomic variation between individuals, and for inferring the transcriptional regulatory pathways that mediate genotype–phenotype relationships. However, these co-expression networks must be interpreted with caution, as they can arise from multiple processes. Here, we investigate one such process, using simulations to demonstrate that hybridization and gene flow between populations can greatly modify co-expression networks. Admixture between populations produces correlated expression between genes experiencing linkage disequilibrium. This correlated expression does not reflect functional relationships between genes but rather depends on migration rates and physical linkage on chromosomes. Given the prevalence of gene flow and hybridization between divergent populations in nature, these introgression effects likely represent a significant force in network evolution, even in populations where hybridization is historical rather than contemporary. These findings emphasize the critical importance of considering both evolutionary history and genomic architecture when analyzing gene co-expression networks in natural populations.