Organophosphorus pesticides(OPs) are widely used in agriculture, which have caused serious environmental pollution and ecological damage. In addition, OPs can accumulate in the organisms through food chain, leading to severe threat to human health. Microbial degradation serves as an efficient tool for remediation of OPs contaminated soils without secondary pollution. At present, the cultivable method is most commonly used for screening OPs-degrading microorganisms, while most microorganisms are uncultivable in the natural ecological environment. Identification of functional microbes with the novel uncultivable technology is becoming a promising technology. This paper, based on the use of OPs and the environmental problems, summarized the migration and transformation patterns of OPs in soils and the identification of the uncultivable functional microbes using the recently developed Stable Isotope Probing (SIP) and magnetic nanoparticle technology, discussed the functional genes for OPs degradation and the degradation pathways as well as the combination of plants and microbes in remediation of OPs-contaminated soils, introduced the limiting environmental factors influencing OPs degradation, including pH, temperature, organic matter content, etc., and finally, put forward the challenges and prospectives of microbial degradation of OPs.