Plant secondary metabolites are important traits that can benefit an invasive plant in its new environment. In the case of rapid evolution in the invaded area, the chemical weapons of introduced plants may diversify, and novel combinations or extreme concentrations of these secondary metabolites may be expressed. The invasive Fallopia species complex (F. japonica, F. sachalinensis, and the F. × bohemica interspecific hybrids) is a good model to assess how chemical traits can vary during post-introduction evolution. We analyzed and compared the composition of secondary metabolite extracts in F. × bohemica hybrids and in the parental species grown in the introduced area. HPLC-DAD profiles were obtained for each Fallopia species, and the main peaks of the HPLC chromatograms represent phenolic compounds. Analyses based on secondary metabolite profiles showed that F. × bohemica hybrids are closer to F. japonica. The F. × bohemica hybrids expressed the compound families described in F. japonica and F. sachalinensis, with quantitative variations between them. Hybrid chemical cocktails showed a diversification of chemical weapons. Furthermore, transgressive segregation was observed. Three dianthrones were identified for the first time in a Fallopia species and were more highly expressed in F. japonica and F. × bohemica hybrids. These results suggest an evolution in the chemical traits of Fallopia taxa in invaded areas such that certain genotypes may well have acquired new chemical cocktails resulting from post-introduction hybridizations.