Native community resistance to plant invasion may reflect microbial effects on invader establishment. Here, we compared the effects of the aboveground and belowground microbes and leaf functional traits of 25 native plant species on the germination and survival of invader Ageratina adenophora. Results show that leaf physical and chemical traits vary among plant species and shape the aboveground microbial community. Local plants more phylogenetically close to A. adenophora harbour more similar pathogen communities to those in A. adenophora. The aboveground tissue inoculations had more adverse effects on A. adenophora establishment by delaying germination time and decreasing the germination rate and seedling survival than did soil inoculations; aboveground tissues from local plants, which are more closely related to A. adenophora, cause longer germination times and greater seedling mortality of A. adenophora. Moreover, local plant aboveground fungi, rather than bacteria, adversely impact seedling survival, and most of the detrimental fungal pathogen ASVs are specialists. Several strains isolated from dead seedlings caused by aboveground tissue inoculations belonging to Alternaria, Fusarium and Stagonosporopsis were verified to kill more than 60% of A. adenophora seedlings and thus have great potential as biocontrol agents for A. adenophora. This is the first study to provide evidence for the effects of phylogenetic relatedness and leaf traits (both functional and microbial) on local community resistance to invaders through the regulation of germination and seedling survival.