Although metagenomics is a relatively new scientific trend, it has managed to become popular in many countries, including Russia, over its 20-year history. This division of molecular genetics studies ecosystem- extracted nucleic acids (DNA and RNA), which contain full information about the microbial community of a habitat. Owing to metagenomic methods, soil microbiology has undertaken to study not only known cultivated types of microorganisms but also noncultivated forms, the biological properties of which can be suggested exclusively from the genetic information coded in their DNA. It turns out that such “phantom” types constitute the overwhelming majority within soil microbial communities; to all appearances, they actively participate in ensuring soil fertility, and, hence, in the opinion of the authors of this paper, study of them is topical for both basic research and agricultural practice. The development of metagenomic technologies will help understand biological phenomena determined by close plant–microbe interactions, such as increasing the productivity of agricultural crops and protecting them against phytopathogens. However, the introduction of new methods has always presented difficulties; in metagenomics, they are associated with the acquisition, storage, and bioinformational analysis of a huge array of genetic information.