John James Audubon was the first person to formally describe the yellow-billed magpie. He named it ""Corvus nuttalli"" to honor the naturalist Thomas Nuttall. Within the genus "Pica", the species is closest to the North American black-billed magpie ("P. hudsonia"). Both species share a common ancestor that migrated from Kamtchatka to Alaska some time in the Pleistocene. Black-billed and yellow-billed magpie diverged as a result of the glaciation of the Rocky Mountains. The yellow-billed yagpie became isolated in the warm climate of California and adapted to it. The species' population was hit hard by the outbreak of the West Nile Virus after 1999. It is currently not considered as endangered, but the virus and the degradation of its habitat pose a serious threat to some populations.