With the development of RNA interference, transgenic crops with double strands RNA to control plant disease are more and more. The transgenic cucumber with mapk (Mitogen-activated protein kinase) dsRNA could inhibit expression of mapk gene of root knot nematode, and had good control efficiency to the nematode. In order to evaluate the ecological safety of this transgenic cucumber and to reveal the effect on the community of soil bacteria, the diversity of soil bacteria in non-transgenic cucumber and transgenic cucumber were revealed by 16S rRNA gene clone library. The result showed that 124 OTUs were obtained from the library of non-transgenic cucumber soil, and 122 OTUs were found from the library of transgenic cucumber soil. 115 OTUs were shared by two libraries. The bacteria in two libraries were belonged to Acidobacteria, Actinobacteria, Armatimonadetes, Bacteroidetes, candidate division BRC1, Chloroflexi, Firmicutes, Gemmatimonadetes, Nitrospira, Planctomycetes, Proteobacteria, Verrucomicrobia and unclassified_Bacteria. The bacteria of Proteobacteria, Bacteroidetes, Chloroflexi and Acidobacteria were dominant groups, and others groups were minority. At class level, the dominant bacteria groups obtained from two libraries were no difference, and the percentage of clones in each class was similar. In the phyla of Acidobacteria and Bacteroidetes, the dominant groups were Acidobacteria_Gp6 and Sphingobacteria. The bacteria of unclassified Chloroflexi and Betaproteobacteria were majority in the phyla of Chloroflexi and Proteobacteria. From the index of diversity, there was no difference in two types of soil. On the whole, the bacterial communities of two types of soil were no difference, and not markedly affected by transgenic cucumber.