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Livestock manure is a major carrier that stores and transmits antibiotic resistance genes (ARGs). The aim of this study was to identify the crucial environmental factors that result in the change in relative abundance of ARGs and MGEs to explore effective methods to reduce the occurrence of ARGs. The abundance of ten ARGs and five MGEs were measured using real-time quantitative PCR with 0, 3, 7, 10, 14, 21, 28, 45, 60, and 75 d in CM and PM aerobic composting. The succession law of the bacterial community was analyzed using 16S rRNA high-throughput sequencing. Furthermore, the abundance of ARGs and MGEs was correlated with the properties (temperature, moisture content, pH, and DOC) of composting piles to identify the crucial factors affecting the variation in ARGs and MGEs. The results showed that the abundance of ARGs and MGEs in PM was higher than that in CM. Composting significantly reduced the relative abundance of nine ARGs and five MGEs. The removal ratios of three ARGs ( tetM, tetT , and aacA ) and four MGEs ( ISEcp1, IS1216, IS613 , and tnp614 ) in CM reached 99%. The removal ratios of nine ARGs[ tetB(P), tetL, tetM, tetO, tetT, aacA, aadD,aphA3 , and sat4 ] and four MGEs ( ISEcp1, IS26, IS1216 , and tnp614 ) reached 99% in PM. However, the abundance of the genes tetG, intI1 , and IS6100 increased. Firmicutes and Actinobacteri a were dominant in CM and PM during composting. Actinobacteria and Proteobacteria may have been the major host bacteria of tetG and intI1 . The redundancy analysis showed that moisture and pH were the crucial factors that could influence the differences in the abundance of ARGs and MGEs. The composition and abundance of ARGs were driven by physicochemical properties, bacterial community, and MGEs. Composting could significantly reduce the abundance of ARGs in CM and PM, thus reducing the risk of ARGs being distributed via livestock manure application. However, some ARGs and MGEs remained in high abundance. Therefore, it is necessary to further optimize the composting process, improve the harmless treatment effect of livestock manure, and promote the safe agricultural use of organic fertilizers.