Ichthyornis is close to the ancestry of modern birds, the Aves, but represents an independent lineage.
It was long believed that it was closely related to some other Cretaceous taxa known from very fragmentary remains — Ambiortus, Apatornis, Iaceornis and Guildavis — but these seem to be closer to the ancestors of modern birds than to Ichthyornis dispar.
In Clarke's 2004 review, the former order Ichthyornithiformes and the family Ichthyornithidae are now superseded by the clade Ichthyornithes, which in the paper was also defined according to phylogenetic taxonomy as all descendants of the most recent common ancestor of Ichthyornis dispar and modern birds.

 
Of the several described species, only one, Ichthyornis dispar, is currently recognized, following the seminal review by Julia Clarke.
Marsh had previously named a specimen now attributed to I. dispar as Graculavus anceps.
Clarke argued that because the rules for naming animals laid out by the ICZN state that a type species for a genus must have originally been included in that genus, Ichthyornis anceps is ineligible to replace I. dispar as the type species and so must be considered a junior synonym even though it was named first.
However, Michael Mortimer pointed out that this is incorrect; while I. anceps cannot become the type species of Ichthyornis, the ICZN does not preclude it from becoming the senior synonym of the type species I. dispar.
Therefore, I. anceps should have been considered the correct name for the only recognized Ichthyornis species.
All other supposed species of Ichthyornis have not been supported as valid.
The presumed "Ichthyornis" lentos, for example, actually belongs into the early galliform genus Austinornis. "
Ichthyornis" minusculus from the Bissekty Formation (Late Cretaceous) of Kyzyl Kum, Uzbekistan, is probably an enantiornithine.
All other Ichthyornis species are synonymous with I. dispar.

The cladogram below is the result of a 2014 analysis by Michael Lee and colleagues that expanded on data from an earlier study by O’Connor & Zhou in 2012.
The clade names are positioned based on their definitions.
Ichthyornis is close to the ancestry of modern birds, the Aves, but represents an independent lineage. It was long believed that it was closely related to some other Cretaceous taxa known from very fragmentary remains — Ambiortus, Apatornis, Iaceornis and Guildavis — but these seem to be closer to the ancestors of modern birds than to Ichthyornis dispar. In Clarke's 2004 review, the former order Ichthyornithiformes and the family Ichthyornithidae are now superseded by the clade Ichthyornithes, which in the paper was also defined according to phylogenetic taxonomy as all descendants of the most recent common ancestor of Ichthyornis dispar and modern birds.
 
Of the several described species, only one, Ichthyornis dispar, is currently recognized, following the seminal review by Julia Clarke. Marsh had previously named a specimen now attributed to I. dispar as Graculavus anceps. Clarke argued that because the rules for naming animals laid out by the ICZN state that a type species for a genus must have originally been included in that genus, Ichthyornis anceps is ineligible to replace I. dispar as the type species and so must be considered a junior synonym even though it was named first. However, Michael Mortimer pointed out that this is incorrect; while I. anceps cannot become the type species of Ichthyornis, the ICZN does not preclude it from becoming the senior synonym of the type species I. dispar. Therefore, I. anceps should have been considered the correct name for the only recognized Ichthyornis species. All other supposed species of Ichthyornis have not been supported as valid. The presumed "Ichthyornis" lentos, for example, actually belongs into the early galliform genus Austinornis. "Ichthyornis" minusculus from the Bissekty Formation (Late Cretaceous) of Kyzyl Kum, Uzbekistan, is probably an enantiornithine. All other Ichthyornis species are synonymous with I. dispar.
The cladogram below is the result of a 2014 analysis by Michael Lee and colleagues that expanded on data from an earlier study by O’Connor & Zhou in 2012. The clade names are positioned based on their definitions.
Ichthyornis