In this lecture an overview of the diversity of bacterial and eukaryotic microorganisms (including protists, fungi, phyto- and zooplankton) and of viruses will be given. The need for a comprehensive and precise taxonomy to structure microbial diversity will be depicted. This includes the explanation of the currently applied taxonomic hierarchy and the methods used in taxonomy. The latter encompasses modern phylogenetic methods based on single genes up to complete genomes. The structure of eukaryotic cells and the evolution of eukaryotes will be explained. Furthermore, characteristics of the various groups of microorganisms will be illustrated and how they are used for classification. Typical habitats and environmental factors having an influence on the distribution and diversification of the various microorganisms will also be demonstrated.