AbstractMotivation: The classification of biological entities in terms of species and taxa is an important endeavor in biology. Although a large amount of statements encoded in current biomedical ontologies is taxon-dependent there is no obvious or standard way for introducing taxon information into an integrative ontology architecture, supposedly because of ongoing controversies about the ontological nature of species and taxa.Results: In this article, we discuss different approaches on how to represent biological taxa using existing standards for biomedical ontologies such as the description logic OWL DL and the Open Biomedical Ontologies Relation Ontology. We demonstrate how hidden ambiguities of the species concept can be dealt with and existing controversies can be overcome. A novel approach is to envisage taxon information as qualities that inhere in biological organisms, organism parts and populations.Availability: The presented methodology has been implemented in the domain top-level ontology BioTop, openly accessible at http://purl.org/biotop. BioTop may help to improve the logical and ontological rigor of biomedical ontologies and further provides a clear architectural principle to deal with biological taxa information.Contact: stschulz@uni-freiburg.de