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This Special Issue will cover research on bacteria and archaea, mitochondria, and plastids. At present, without genetic studies, it would be impossible to imagine research on unculturable microorganisms, the relationship and taxonomic position of microbes, and the identification of genetically determined diseases at the mitochondrial level, and much more. The applications of genomics are closely intertwined with advances in other areas of biology. One example is the process of describing new prokaryotic taxa, for which molecular biologists, biochemists, and microbiologists combine phenotypic and biochemical studies with genomic sequence analysis. This issue welcomes articles on the study of the genetic structures of the above organisms, the development of new methods in this direction, and the discovery of new systems and functions in organisms that are important for their life activity. In addition, many protein structures have become of interest due to advances in the study of genomes and individual genomic clusters. Therefore, reports on the discovery of new proteins in this way with both known and new functions are welcome. Overall, we strongly believe that advances in genomic studies of the listed entities will lead to reports of new gene discovery, new knowledge about the products of these genes, and new capabilities of the organisms possessing these genes. This Special Issue aims to provide an overview of recent advances in genetic research on cellular organelles and one of the simplest life forms, prokaryotes, as well as the impact of these advances on adjacent problems.