Ageratina adenophora is considered one of the most problematic invasive species in Nepal. Tropical to subtropical Nepal forests are severely invaded by this species. Previous studies on A. adenophora are concentrated on crop plants and some weedy herbs but the studies on its effects on native trees have been very scarce. Moreover, previous tests have typically used crushed or ground leaves that may contain compounds that do not exist on soil surface. To avoid these drawbacks, we used different bioassays to investigate the modes of impacts of A. adenophora on native trees (Schima wallichii and Alnus nepalensis) in Nepal. Seedlings of these tree species were grown in A. adenophora invaded and uninvaded soils, soil with A. adenophora litter and without litter, and soil with extracts prepared by soaking intact A. adenophora leaves. Analysis of growth parameters showed that litter, extracts and invaded soil by A. adenophora were toxic to the native seedlings. Inhibition was shown after seedling exposure and the effect remained permanent. In conclusion, native tree species are vulnerable to A. adenophora invaded sites creating problems in the establishment and survival of native seedlings in Nepal forests.