系統和應用微生物學涉及微生物多樣性和原核生物系統學的各個方面。它主要研究細菌和古細菌；只有在少數情況下才會考慮真核微生物。該雜志對微生物多樣性有著廣泛的理解，并鼓勵提交以下微生物學分支的手稿：系統學：涉及分類和分類學的理論和實踐問題，即：（i）原核生物類群的新描述或修訂，包括念珠菌類中尚未培養的類群的描述；（i i）確定分類和系譜關系的創新方法；（i i i）分類內的評價。多學科方法的多樣性；（iv）識別方法。

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.