Chemical signals are crucial in mediating ecological and evolutionary adaptation of plants to their environments. Invasive plants can release distinct secondary metabolite mixtures in their new ranges, enhancing their mutualistic interactions and improving their performance, but genetic mechanisms of such adaptations are unexplored. We used Triadica sebifera plants to investigate evolutionary changes in chemical signals (flavonoids and strigolactones) that enhance arbuscular mycorrhizal (AM) fungal associations. We found plants from invasive populations produced higher concentrations of the flavonoid quercetin and the strigolactone 5-deoxystrigol, and had higher AM fungal colonization rates and biomass, relative to those from native populations. Also, applications of either chemical increased AM fungal colonization. Higher expression of genes in flavonoid (FLS) and strigolactone (CCD8) biosynthesis pathways that increased levels of quercetin and 5-deoxystrigol, respectively, were confirmed. These results provide insights into genetic mechanisms that contribute to higher AM fungal colonization and plant invasion success.