In an international collaboration we investigated the evolution of tissue-specific genes in the Lacerta viridis complex (European green lizard). We had sequenced and analyzed the genomes of three species/lineages and detected gene flow between the Adriatic lineage and L. viridis, suggesting that the evolutionary history of the L. viridis complex is likely shaped by gene flow. Genes highly expressed in the ovaries experienced accelerated evolution presumably contributing to establishing reproductive isolation in the Lacerta viridis complex. In addition, we built co-expression networks and found that genes that are strongly co-expressed in the brain also show accelerated evolution, potentially pointing to the evolution of behavioral differences between the species. Such accelerated evolution of tissue-specific genes might allow for speciation amidst gene flow in European green lizards.