Soil microbial diversity is considered to be critical to the maintenance of soil health and quality, and agricultural practices influence soil microbial diversity and the ability to suppress plant diseases (Garbeva et al. 2006). However, few reports have described the community of microorganisms after application of different organic fertilizers and biocontrol agents to soils in which cucumbers are cultivated. Luo et al. (2010) found that the application of a bio-organic fertilizer decreased the diversity of fungi in the rhizosphere of cotton. In this study, we found that applications of N43 and BIO increased bacterial diversity in the rhizosphere of cucumber seedlings but did not change fungal diversity. This could have been caused by the use of different biocontrol agents and plant growth periods.