Its remains, consisting of two partial humeri, were recovered from an upper Paleocene deposit in Kazakhstan.

[1] The relationships of this genus are unknown; it was initially placed in the Presbyornithidae, which at that time were believed to be some sort of "transitional shorebird".

Upon recognition that the presbyornithids were more likely a prehistoric lineage of fairly advanced waterfowl, Zhylgaia was assigned to the form taxon "Graculavidae", an assemblage of Late Cretaceous and Paleocene shorebirds which are not a natural clade but merely an assemblage of superficially similar birds.

[citation needed] In 2008, Zhylgaia was assigned to Prophaethontidae—an extinct family related to modern tropicbirds—on the basis of its anatomy and size closely matching the prophaethontid Lithoptila.

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