This genus is considered especially close to Cyanolyca, an upland radiation occurring throughout the American Cordillera from Mexico to Peru and Bolivia, who look very similar to the blue-and-black species of Cyanocorax except for being a bit smaller.

[2] Cyanocorax jays are generally black-and-blue, often with considerable amounts of white plumage, but brown or yellow to green in a few species.

The Tufted jay, the northwesternmost member of this genus, seems to be a distinct fourth and ancient branch of this radiation, perhaps a remnant of an early expansion that largely went extinct as the Cissilopha lineage displaced it.

[2] The fossil corvid Protocitta dixi, described from Middle Pleistocene (Illinoian, Penultimate Glacial Period, roughly 150.000 years ago) remains found in a former cave near Reddick, Florida, was described as similar to both Calocitta and Psilorhinus lineages.

Although no cladistic analysis was conducted, at least qualitatively it was assessed as less closely related to the Holarctic magpies, who are a member of the "monochrome" radiation of crows and ravens, so it is very likely that Protocitta was indeed a prehistoric American blue jay.