Charles Darwin commented that Ichthyornis, as one of the “toothed birds” from the Late Cretaceous of Kansas, offered some of “the best support to the theory of evolution” (in litt., C. Darwin to O.C. Marsh, August 31, 1880). Ichthyornis figures no less prominently today. It is one of the closest outgroups to crown clade Aves, and remains one of the only Mesozoic avialans known from more than a handful of specimens. As such, Ichthyornis is an essential taxon for analyses of deep divergences within Aves because of its influence in determining the morphologies ancestral to the crown clade.

Ichthyornis, however, has languished in need of new anatomical description and taxonomic revision. Many of the best Ichthyornis specimens were largely inaccessible, plastered into Yale Peabody Museum (YPM) exhibit mounts for nearly a century. The focus of this study was the entire YPM Ichthyornis collection, the largest at any institution.

The elements removed from the mounts were identified to the specimens with which they were originally associated. Detailed morphological study of the 81 YPM specimens yielded the following results: (1) there is evidence for only one species of Ichthyornis, rather than the eight previously proposed; (2) 78 specimens are part of this species, Ichthyornis dispar; (3) two previously identified species are not part of Ichthyornis; and (4) one new species is identified. This analysis also provided a case study in the application of phylogenetic nomenclature at the species level. The morphology of Ichthyornis dispar is described in detail from the holotype and referred specimens.

Phylogenetic analyses of 202 morphological characters, scored for 24 terminal taxa, evaluated the relationships among Mesozoic ornithurines including Ichthyornis dispar and the newly identified taxa. Analysis of 23 core taxa produced two most parsimonious trees (L: 384, CI: 0.66). Marsh's “Ichthyornithiformes” is not monophyletic: Two previously named species of Ichthyornis as well as Apatornis celer are placed as more closely related to or as part of Aves. The results of the phylogenetic analyses have implications for previous hypotheses of the timing and pattern of the origin of Aves.