A total of 247 clones of 16S rRNA genes from microorganisms captured by 0.2- and 0.1-μm-pore-size filters from sedimentary and granite rock aquifers were amplified and yielded 37 operational taxonomic units (OTUs). Fifteen OTUs captured by 0.1-μm-pore-size filters were affiliated with the candidate divisions OD1 and OP11, representing novel lineages. On the other hand, OTUs captured by 0.2-μm-pore-size filters were largely affiliated with Betaproteobacteria. Molecular techniques phylogenetically characterize the microbial communities filterable by 0.2-μm-pore-size filters, and a Mediterranean community was thus affiliated with Alphaproteobacteria, Gammaproteobacteria, and Cytophaga-Flavobacterium-Bacterioides On the other hand, few or no studies have focused on the microorganisms in deep groundwater that are filterable by 0.2-μm-pore-size filters. We have characterized the microorganisms captured by 0.2- and 0.1-μm-pore-size filters in deep groundwaters of the Tono uranium mine, Japan (35.4°N, 137.2°E), where total counts of cells captured by 0.2-μm-pore-size filters are in the range of 105 to 106 ml−1