Systematic biology is concerned with the study of biodiversity. Systematic biology is mostly considered to be a synonym of taxonomy and both terms will be used in this text in the same sense. However, some authors consider systematic biology to be broader subject encompassing all the aspects of study of biodiversity, including the diversity of biological structures and functions, while taxonomy is understood in a narrower sense as a discipline attempting to catalogue all species, to arrange these species in systems of usually hierarchically ordered groups and naming of these groups in accordance with the rules and recommendations of taxonomic nomenclature. Species can basically be classified in a system of broader and broader (i.e. higher and higher) taxa in three ways, i.e. on the basis of similarity, of phylogenetic relatedness or of both similarity and relatedness. Biologists now generally agree that the basis for classification of organisms, i.e. creation and naming of the individual specific taxa, should be the reconstructed phylogenesis of the studied phylogenetic lines. Thus the subjects of phylogenesis and classification of organisms are usually combined. Although phylogenetics, i.e. the study of phylogenesis, and classification of organisms, including the formation of taxa, are very closely related, they are, in fact, two different disciplines. Because each of them has different goals and somewhat different methodical instruments, they can follow somewhat different principles in some areas. Lack of consideration of these aspects is probably the reason for a great many misunderstandings and controversies amongst the proponents of two of the currently most influential areas of taxonomy, phylogenetic taxonomy (i.e. cladistics) and evolutionary taxonomy (i.e. eclectic systematics). This chapter will be concerned with the general laws, basic rules and most important aspects of the creation of a taxonomic system.