Pesticides play an important role in preventing insect pests and weeds in crops. However, excessive use of pesticides has been known to be unsafe, due to their toxicity to non-target organisms and the ecosystem. Biodegradation is an innovative approach for decontaminating pesticide pollution. However, compared with the list of extensively used pesticides there are few well-characterized strains of microbes that transform pesticides into less-toxic or more labile products at environmentally useful rates. Fortunately, the technology required to isolate and characterize such microbial strains has improved immensely in the recent years. Furthermore, recent experimental developments have made practical the modification of potentially beneficial biodegradation genes so that they may be optimally expressed in a wide range of microbial species. This reviews article explore the recent studies that have focused on biodegradation of pesticide residues, the mechanism of microbial degradation of pesticides, the factors that affect the degradation of pesticides and the new application of microbial degradation of pesticides.