The aggregation of antibiotic resistance genes (ARGs) in agro-ecosystems and their potential transmission into the food chain represents a serious threat to public health. However, we have very limited knowledge of the pathways and mechanisms for transmission of antibiotic resistance from the soil to vegetables following land application of animal manures. Here, we constructed a glasshouse pot experiment to explore the impacts of poultry or cattle manure application on the patterns of resistome and microbiome in the rhizosphere, endosphere and phyllosphere of the harvestedlettuce and cherry radish. In total, 145 ARGs and 10 MGEs were detected in all the samples. Manure application increased the ARG diversity and abundance in bulk soil, rhizosphere soil, phyllosphere and root endophyte for both lettuce and cherry radish. Moreover, phyllosphere and endophyte shared a large number of ARGs with manure and soil, suggesting that manured soil was an important source of ARGs detected in vegetable samples. Procrustes and network analysis suggested that the profile of ARGs was strongly affected by bacterial community compositions and four bacterial phyla were identified as potential hosts of ARGs.Our study suggests that vegetables grown in manure-amended soils are at risk of contamination by manure-borne antibiotic resistant bacteria.