While magpie-jays (Calocitta) have long been treated as a distinct genus, their affinities, especially with Brown Jay (Psilorhinus morio) have been up for some debate. Within the Corvidae, they belong to the New World Jays. They have long been allied with Cyanocorax, usually as a sister taxon (Hope 1989; de los Montero and Cracraft, 1997; Saunders & Edwards, 2000), but the relationship of Psilorhinus and Cyanocorax has been unstable. The most recent findings place Calocitta as the sister taxon to Psilorhinus, with this clade nested within what is currently defined as Cyanocorax and related to a suite of South American Cyanocorax, as opposed to any of a number of Central American species (Bonaccorso and Peterson, 2007; Bonaccorso et al., 2010). The overall relationship of this clade to Cyanocorax raises the possibility that both genera will be subsumed into a greater Cyanocorax.
The white-throated magpie-jay has been documented to hybridize with two species, both close relatives. Reports exist of hybrids with black-throated magpie-jay (Calocitta colliei) in Jaliscon, Mexico. More rarely, C. formosa appears to hybridize with its sister genus, Psilorhinus. A specimen almost certainly with P. morio has been documented from near Tuxtla Gutierrez, Chiapas, Mexico (Pitelka et al. 1955) and in Guanacaste, Costa Rica a mixed pair was observed raising young (Elena C. Berg, personal communication).