This study explored the effect of Eisenia fetida on the soil bacterial community structure, to facilitate selecting earthworms to improve soil quality. After 10 days of incubation by E. fetida in both lateritic red and paddy soil, 16S rDNA Illumina Miseq high-throughput sequencing technique was employed to analyze the bacterial community structure compositions and diversities of the soils with or without earthworms. Sequence splicing and statistical analysis of OTU abundance were calculated by FLASH and UCHIME, and OTU species classification and Alpha community abundance index were analyzed using R and mothur. The results showed that the bacterial community structure of the soils with earthworms varied, compared to that of the soils without earthworms, indicating that E. fetida changed the soil bacterial community structure. In lateritic red soil, 5 non-dominant phyla were newly added at the presence of the earthworms, which were FBP, Fibrobacteres, OP11, Tenericutes and Thermi. In addition, it could be observed that Cytophagia, Spartobacteria and Verrucomicrobiae in lateritic red soil incubated by E. fetida turned into dominant classes, while Solibacteres became a non-dominant class (Fig. 2 & Fig. 3). In paddy soil that incubated with E. fetida, it was noted that Poribacteria was newly added as a non- dominant phylum, that Spirochaetes became a dominant phylum, as well as that the non-dominant phyla involving SBR1093, SC4, WS4 and WS5 died out (Fig. 4). Besides, Spirochaetes and Verrucomicrobiae became dominant classes while Planctomycetia declined to be a non-dominant class (Fig. 5). In general, the dominant bacteria in both lateritic red and paddy soil with the incubation of E. fetida included Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Firmicutes, Planctomycetes, Proteobacteria and Verrucomicrobia (Fig. 2 & Fig. 4). The relative abundance of Acidobacteria significantly decreased by 44.90% but the relative abundance of Bacteroidetes significantly increased by 14.88% in the lateritic red soil with the incubation of E. fetida (Table 3). In contrast, the relative abundances of Acidobacteria, Chloroflexi, Gemmatimonadetes, Nitrospirae, Planctomycetes and Verrucomicrobia significantly decreased by 49.05%, 20.44%, 64.01%, 35.00%, 33.56% and 24.38% respectively while Bacteroidetes and Spirochaetes significantly increased by 28.85% and 154.17% in the paddy soil incubated by earthworms (Table 4). The variations on the abundances of the bacteria in the two types of soils were different. In detail, it was increased in lateritic red soil but decreased in paddy soil at the presence of the earthworms. Moreover the bacterial diversities in both lateritic red and paddy soils decreased (Table 5). It revealed that E. fetida changed the community structure compositions and diversities of bacteria in the two types of soils and thus this study offered a theoretical foundation for further understanding of earthworm digestion and its interactions with microorganisms.