This study evaluates the relative contributions of leaves and roots to the belowground allelopathic effects of Mikania micrantha. The hypothesis that leaves contribute more to the allelopathic effect than roots was experimentally tested. We assessed the allelopathic effects of aqueous extracts from Mikania leaves and roots on the seed germination and seedling growth of two co-occurring woody plants in southern China, Lagerstroemia indica L. and Robinia pseudoacacia L. The results showed that the aqueous extracts from Mikania leaves and roots had inhibitory effects on the woody species. Allelopathic activity depended on the concentration of the extracts, target species, and the extract sources (i.e., leaves vs. roots of Mikania). Leaf extract showed stronger allelopathic effects than root extract on germination percentage, initial germination time, speed of germination, and shoot height; while root extract had greater allelopathic effects on roots than leaf extract. The latter phenomenon might greatly promote the invasion success of Mikania due to more direct and effective allelopathy of root. Our results suggest that allelopathy of root extract on belowground biomass might be greater than that of leaf extract for some species in contrast allelopathy of leaf extract on belowground biomass might also be greater than that of root extract for other species, at least for their effects on root growth of the target species.