Scope of the Journal: Systematic and Applied Microbiology deals with various aspects of microbial diversity and systematics of prokaryotes. It focuses on Bacteria and Archaea; eukaryotic microorganisms will only be considered in rare cases. The journal perceives a broad understanding of microbial diversity and encourages the submission of manuscripts from the following branches of microbiology:

Systematics: Theoretical and practical issues dealing with classification and taxonomy, i.e. (i) new descriptions or revisions of prokaryotic taxa, including descriptions of not-yet cultured taxa in the category Candidatus (ii) innovative methods for the determination of taxonomical and genealogical relationships, (iii) evaluation of intra-taxon diversity through multidisciplinary approaches, (iv) identification methods.

Applied Microbiology: all aspects of agricultural, industrial, and food microbiology are welcome, including water and wastewater treatment.

Comparative biochemistry and genomics: studies concerning biochemical/metabolic and genomic diversity of cultured as well as yet-uncultured Bacteria and Archaea.

Ecology: descriptions of the microbial diversity in natural and man-made ecosystem; studies quantifying the size, dynamics, and function of microbial populations; innovative research on the interaction of micro-organisms with each other and their biotic and abiotic environment.