Phylogeny is concerned with the evolutionary diversification of organisms or groups of organisms. A group of organisms with a name is called a taxon (singular). Taxa (plural) can span different levels of the evolutionary hierarchy. For instance, the group containing all birds is a taxon (comprising the class Aves), and the group of all species of daisies (the genus Bellis) is a taxon. Phylogenies can likewise include just one genus (i.e., depict species relationships) or span an entire kingdom.

Typically, phylogeny is represented by a tree called a phylogenetic tree. It is a branching diagram that shows the evolutionary relationship between different organisms, with the most closely related species being grouped together. Each taxon of interest is depicted at the tip of the branch, and the branches represent the relationship between these taxa. Closely related taxa share a larger portion of their genome, resulting in morphological similarities. Sister taxa share an immediate common ancestor, represented by a shared node.

Nodes in the tree depict a morphological characteristic or molecular change that differentiates taxa. All taxa that directly connect to a specific node share a recent common ancestor. Hence, the root of the tree is the ancestor shared by all taxa in the tree. A lineage that evolved early from the root and remained unbranched is called a basal taxon. A tree without a root represents the relationship of taxa but does not provide information on the shared common ancestor.

The length of the branches of a tree may or may not have a meaning. In a scaled tree, the length of the branch may either represent time or the number of changes that occurred since the taxa evolved from a common ancestor.