[Objective] To investigate the influence of complex microbial agent on the soil bacterial populations in apple replanted orchard. [Methods] After the treatment with complex microbial agent, soil specimens were sampled from new crop and replanted apple orchard then analyzed by the method of automated ribosomal intergenic spacer analysis to monitor the bacterial community. [Results] Two years after treatment with complex microbial agent, the operational taxonomic units (OTUs) and Shannon-Wiener diversity index of replanted orchard was 250 and 4.44, respectively. In comparison, corresponding values were 234 and 3.81 in new crop orchard. One-Way ANOSIM analysis further showed that the difference coefficient was 0.108 3 and 0.084 3 respectively. In addition, the new crop and replanted orchard shared 89 core OTUs, and had a moderate similarity (corresponding Jaccard community similarity coefficient was 0.47). [Conclusion] The application of complex microbial agent could improve the soil microbial diversity and benefits to the recovery of the soil microbial ecosystem in replanted orchard.