Integrating and querying biological data across organisms, whether on small or large scales, to this day relies on traditional names for organisms and groups of organisms based on Linnaean nomenclature. However, when it comes to integrating and communicating data, these suffer from two major limitations. Firstly, because they are simple text-strings, machines cannot access the meaning intended by those who coin a name and those who apply it, resulting in rampant ambiguity and inconsistency in what organism names are interpreted to mean. Secondly, there are many groups of organisms for which a Linnaean name does not and may never exist, but for which valuable biological knowledge needs to be communicated. The Phyloreferencing project aims to address these challenges by defining ontology-based references (“phyloreferences”) to elements on the Tree of Life that are unambiguous and have fully computable semantics defined by patterns of evolutionary relatedness. The mechanism that this project will develop uses standards and tools developed for the Web, specifically the Web Ontology Language (OWL), ontologies, and machine reasoning. Specifically, this work aims to develop phyloreferences as OWL class expressions consisting of sufficient and necessary conditions, which machine reasoners can use to identify subclasses and class instances. Ontology and reasoning technologies have already shown their power for biological knowledge integration and discovery and are increasingly being adopted for evolutionary research as well.