The motivation for the development of phylogenetic nomenclature (originally called “phylogenetic taxonomy”) was to allow biological classification (or “systematization”) to represent phylogenetic relationships, and to embody important principles such as “the untenability of paraphyletic groups” (de Queiroz and Gauthier 1990). From this starting point de Queiroz and Gauthier developed a creative new basis for systematization in which the entities are not ranked taxa but clades (de Queiroz and Gauthier 1990, 1992, 1994; de Queiroz 1992, 1994). Instead of attaching names to taxa by reference to a type and a rank, as in traditional biological nomenclature, phylogenetic nomenclature labels taxa by the use of multiple “specifiers” – specimens or apomorphic traits that unambiguously refer to a particular monophyletic taxon. The subsequent development of phylogenetic nomenclature included formation of a scholarly society, the International Society for Phylogenetic Nomenclature, and development of a formal Code, the PhyloCode (http://www.phylocode.org), that is now in final preparation for publication at University of California Press. The hope for many phylogenetic systematists was for a new system of nomenclature that would firmly connect taxonomy to phylogeny and would allow for more stable ways to name the many significant clades that make up the Tree of Life. However, a major challenge for the development of the PhyloCode has been the treatment of species. We argue in this paper that the approach taken to species in the PhyloCode is at odds with the motivations that drove many to support phylogenetic nomenclature and that these problems should be fixed before the PhyloCode is published and officially implemented.