【Objective】 Biosynthetic nano-selenium (SeNP), as a new type of functional fertilizer, has been widely applied into selenium-enriched agricultural production. To date, the effects of SeNP on antibiotic resistance genes (ARGs) and their host microbes in different types of soil are not well understood. This study was designed to investigate the effects of SeNP on the abundance of ARGs and bacterial community structure in the rhizosphere soil of Brassica rapa L. growing in different types of soil. 【Method】 Pot experiments were conducted to analyze the effects of foliar application of different concentrations of SeNP on plant growth, soil properties, bacterial community structure, and the abundance of ARGs and mobile genetic elements (MGEs) in two types of soils (neutral and alkaline). 【Result】 The results showed that foliar application of 1-5 mg·L^–1 SeNP could effectively improve the growth indicators of plants and the content of alkaline hydrolyzable nitrogen in the rhizosphere soil. Compared with the control, the bacterial community abundance in neutral soil increased by 27.09%, significantly. In contrast, the bacterial community abundance in alkaline soil decreased by 14.56%, significantly. And the absolute abundance of ARGs and MGEs also decreased significantly compared to the control group. Foliar application of SeNP not only promoted the increase in the relative abundance of beneficial bacteria (i.e., Gemmatimonadetes, Nitrospirae, and Acidobacteria) in different soils, but also reduced the abundance of potential host bacteria (Chloroflexi) for ARGs in alkaline soil. 【Conclusion】 Biosynthetic SeNP can be served as a potential candidate material to control the spread of soil ARGs effectively. However, the impacts of SeNP on soil antibiotic resistance may vary with different soil types. Thus, further evaluation should be carried out in combination with the characteristics of field soil, providing a reference for the efficient and safe application of SeNP in agricultural production.