With new antibiotics slowing down in development and antibiotic resistant genes (ARGs) popping up and spreading rapidly, antibiotic resistant bacteria (ARB) and ARGs have become imminent threats to public health and a global problem urgently calling for solution. Nowadays, the industry of livestock breeding still abuses the use of veterinary antibiotics in concentrated feeding operation in an attempt to improve growth and control diseases. It is estimated that approximately 30%~50% of the administered antibiotics are excreted with waste instead of being absorbed by animals. Manure is commonly used as a substitute for inorganic N and P fertilizers for agricultural crops, especially in organic farming. In 2013, a total of 54 000 tons of 36 antibiotics was excreted in China, 54% into the soil and 46% into the water environment. The antibiotics involved include sulfonamides, tetracycline, fluoroquinolones, macrolides, β-lactam, etc. The ARGs contained in the ARB excreted with manure, generated in microbes as a result of accumulation of antibiotics in soil, and multiplied with the proliferation of ARGs-containing microbes stimulated by manure are the main sources of ARGs in the soil. Bacterial communities in manure and in soil vary sharply in structure. The bacteria in feces can survive in soil for weeks to months, depending on soil and environment, however, horizontal gene transfer from these bacteria to indigenous soil bacteria might rely on persistence of ARGs in soil. As one of the largest and most diverse microbial habitats on earth, soil has been the source of most discovered ARGs, supplying ARGs to water environment, crops, and animals and human through food chain. Once ARB and their corresponding suite of ARGs enter the soil, water and crops, their persistence and fate depend on nature and viability status of their host bacteria and their living environment. Both natural factors, like temperature, rainfall, time and soil type, and human factors, like content and specie of antibiotic, type and treatment of manure, content of heavy metal and biochar addition, could affect persistence and diffusion of ARGs in soil. However, the impacts of manure application contaminating the soil with ARGs on environmental quality and human health still remain unclear. It is, therefore, suggested that studies should be intensified on modelling, source tracing, biogeographical distribution, rules of ARGs transferring from sources to environmental media, measures to reduce and mechanisms of reducing the transfer, which will help to recycle animal waste safely and control pollution of ARGs in the environment effectively.