Phylogenetic nomenclature is a method of nomenclature for taxa in biology that uses phylogenetic definitions for taxon names. This contrasts with the traditional method, by which taxon names are defined by a type, which can be a specimen or a taxon of lower rank, and a description in words. Phylogenetic nomenclature is regulated currently by the International Code of Phylogenetic Nomenclature (PhyloCode).

Phylogenetic nomenclature associates names with clades, groups consisting of an ancestor and all its descendants. Such groups are said to be monophyletic. There are slightly different methods of specifying the ancestor, which are discussed below. Once the ancestor is specified, the meaning of the name is fixed: the ancestor and all organisms which are its descendants are included in the taxon named. Listing all these organisms (i.e. providing a full circumscription) requires the complete phylogenetic tree to be known. In practice, there are almost always one or more hypotheses as to the correct relationship. Different hypotheses result in different organisms being thought to be included in the named taxon, but application to the name in the context of various phylogenies generally remains unambiguous. Possible exceptions occur for apomorphy-based definitions, when optimization of the defining apomorphy is ambiguous.

Phylogenetic nomenclature assigns names to clades, groups consisting solely of an ancestor and all its descendants. All that is needed to specify a clade, therefore, is to designate the ancestor. There are a number of methods of doing this. Commonly, the ancestor is indicated by its relation to two or more specifiers (species, specimens, or traits) that are mentioned explicitly. The diagram shows three common ways of doing this. For previously defined clades A, B, and C, the clade X can be defined as:

Several other alternatives are provided in the PhyloCode, (see below) though there is no attempt to be exhaustive.

Phylogenetic nomenclature allows the use, not only of ancestral relations, but also of the property of being extant. One of the many methods of specifying the Neornithes (modern birds), for example, is:

Neornithes is a crown clade, a clade for which the last common ancestor of its extant members is also the last common ancestor of all its members.

For the PhyloCode, only a clade can receive a "phylogenetic definition", and this restriction is observed in the present article. However, it is also possible to create definitions for the names of other groups that are phylogenetic in the sense that they use only ancestral relations based on species or specimens. For example, assuming Mammalia and Aves (birds) are defined in this manner, Amniotes could be defined as "the most recent common ancestor of Mammalia and Aves and all its descendants except Mammalia and Aves". This is an example of a paraphyletic group, a clade minus one or more subordinate clades. Names of polyphyletic groups, characterized by a trait that evolved convergently in two or more subgroups, can be defined similarly as the sum of multiple clades.

Using the traditional nomenclature codes, such as the International Code of Zoological Nomenclature and the International Code of Nomenclature for algae, fungi, and plants, taxa that are not associated explicitly with a rank cannot be named formally, because the application of a name to a taxon is based on both a type and a rank. Thus for example the "family" Hominidae uses the genus Homo as its type; its rank (family) is indicated by the suffix -idae (see discussion below). The requirement for a rank is a major difference between traditional and phylogenetic nomenclature. It has several consequences: it limits the number of nested levels at which names can be applied; it causes the endings of names to change if a group has its rank changed, even if it has precisely the same members (i.e. the same circumscription); and it is logically inconsistent with all taxa being monophyletic.^{[citation needed]}