More than 99% of microorganisms on the earth are unculturable with known culturing techniques. The emergence of metagenomics with high-throughput sequencing technologies has enabled researchers to capture a comprehensive view of a complex bacterial community which comprises both culturable and unculturable species. However, the function of an individual species remains difficult to elucidate in a conventional metagenomic study, which generates numerous genomic fragments of unidentifiable origins at a species or genus level. This limitation hampers any in-depth investigations of the community and its unculturable bacterial members. Recently, as an alternative or compensatory approach, genomics targeting a single unculturable bacterial species in a complex community has been proposed. In this approach, whole-genome amplification technique using Phi29 DNA polymerase is applied to obtain a sufficient quantity of DNA for genome sequence analysis from only a single to a thousand bacterial cells. It is expected that a combination of the conventional metagenomics and this single-species-targeting genomics provides a great progress in understanding of the ecology, physiology, and evolution of unculturable microbial communities.