Secondary compounds can contribute to the success of non-native plant species if they reduce damage by native herbivores or inhibit the growth of native plant competitors. However, there is opposing evidence on whether the secondary compounds of non-native plant species are stronger than those of natives. This may be explained by other factors, besides plant origin, that affect the potential of plant secondary compounds. We tested how plant origin, phylogeny, growth strategy and stoichiometry affected the allelopathic potential of 34 aquatic plants. The allelopathic potential was quantified using bioassays with the cyanobacterium Dolichospermum flos-aquae. The allelopathic potential showed a strong phylogenetic signal, but was similar for native and non-native species. Growth strategy was important, and emergent plants had twice the allelopathic potential as compared to submerged plants. Furthermore, the allelopathic potential was positively correlated to the foliar carbon-to-phosphorus (C:P) and total phenolic content. We conclude that eudicot plant species with an emergent growth strategy and high plant C:P ratio exhibit a high allelopathic potential. Unless non-native plant species match this profile, they generally have a similar allelopathic potential as natives.