The beneficial effects of Eisenia fetida on soil properties have been attributed to their interaction with soil microorganisms. The bacterial diversity of the intestinal tract of E. fetida was investigated by culture-dependent and culture-independent methods including denaturing gradient gel electrophoresis (DGGE) and pyrosequencing analyses. In a pure culture, Lysinibacillus fusiformis (51%), Bacillus cereus (30%), Enterobacter aerogenes (21%), and L. sphaericus (15%) were identified as the dominant microorganisms. In the DGGE analyses, B. cereus (15.1%), Enterobacter sp. (13.6%), an uncultured bacterium (13.1%), and B. stearothermophilus (7.8%) were identified as the dominant microorganisms. In the pyrosequencing analyses, Microbacterium soli (26%), B. cereus (10%), M. esteraromaticum (6%), and Frigoribacterium sp. (6%) were identified as the dominant microorganisms. The other strains identified were Aeromonas sp., Pseudomonas sp., Borrelia sp., Cellulosimicrobium sp., Klebsiella sp., and Leifsonia sp. The results illustrate that culture independent methods are better able to detect unculturable microorganisms and a wider range of species, as opposed to isolation by culture dependent methods.