Philosophical arguments have played an influential role in the development of phylogenetic systematics - the field of biology that seeks to reconstruct the genealogical relationships among species, discover the pattern of events that has led to the distribution and diversity of life, and use this knowledge to construct natural classifications of species. Three sets of discussions clearly demonstrate this connection between philosophy and phylogenetics: inference modes and their relevance to competing phylogenetic methods, the nature and treatment of species and higher taxa, and the nature and treatment of phylogenetic evidence (character data). Within each of these areas, systematists have used philosophical arguments to defend particular concepts and methodological approaches, or to propose new ones. And, within each of these areas, philosophers have scrutinized the arguments of systematists and contributed their own.

Vigorous debate amongst systematists regarding these topics is pervasive. A common underlying tension that helps drive such debates revolves around the proper roles of process theories, assumptions, and trained judgment in phylogenetics research. For example, concerns about objectivity and testability have sometimes led systematists to reject methods that depend on evolutionary process theories, but such rejections typically do not 'stick' for very long. Thus, a cyclical pattern is evident - attempts to infuse theoretical dependence into phylogenetics research have repeatedly been countered by charges of non-objectivity and decreased testability, yet attempts to avoid them have repeatedly been countered by charges of operationalism.