Soil bacteria play an important ecological role in the ecosystem of soil in greenhouse and in the exchange of energy and substance, and have a significant inter- or intra interaction between bacterial community and greenhouse crops. Understanding of the composition of soil bacterial communities is benefit to reveal the relationship between the change of land use and the effects of entironment. In this study, total microbial genomic DNA from soil was extracted and purified by density gradient centrifugation, and 16S rRNA gene was amplified using universal primer, 27F and 1492R, and the product of PCR was recycled, ligated, transformed and screened using blue-white selection, and then was constructed 16S rRNA gene clone library. Partial total DNA from soil was treated with end repairing, ligated to Fosmid vector, PCC2FOS, packed using lambda packaging extracts, transfected with E.coli EPI300, and then was constructed metagenomic Fosmid library. The result showed that the 16S rRNA gene clone library was dominated by bacteria belonged to γ-Proteobacteria, which followed by Firmicutes, especially Bacillus, which constituted 32.2% of 16S rRNA gene clone library. The groups including α-Proteobacteria,δ-Proteobacteria and Actinomycetales were minority in the 16S rRNA gene clone library. In addition, 35 OTUs were obtained from the 16S rRNA gene clone library according to sequences similarity of 97%. From the result of end sequencing from metagenomic library, γ-Proteobacteria and Firmicutes were also dominant groups, which constituted 26.1% and 19.8%, respectively. At the level of class, the results from 16S rRNA gene clone library and metagenomic library were also included γ-Proteobacteria,α-Proteobacteria,δ-Proteobacteria,β-Proteobacteria, Actinomycetales and Firmicutes, but the proportions of each class were various, especially Actinomycetales, which contained 2 clones from 16S rRNA gene clone library and constituted 0.7%, but contained 26 clones from metagenomic library and constituted 8.7%. In terms of predominant genus, the numbers of genus from end sequencing were higher than that of 16S rRNA gene clone library（40>35）. In term of dominant bacteria, the two methods both showed that Bacillus was predominant group. However, the result from end sequencing of clone from metagenome contained some minority of bacterial groups, which were not revealed by 16S rRNA gene clone library, such as Gemmatimonadetes, Chloroflexi, CFB group bacteria, Planctomycetes, Verrucomicrobia and Cyanobacteria. This discrepancy maybe reflected the substantial difference in two methods and probably results from the defects of 16S rRNA gene method, including PCR bias, chimeric gene, heteroduplex and mutation and so on. Comparing of bacterial community of the exposed soil, the bacterial diversity of soil in greenhouse was relatively low. This phenomenon was possibly directly caused by continuous cropping and single cropping.