The black-throated magpie-jay was formally described in 1829 by the Irish zoologist Nicholas Aylward Vigors from a specimen collected at San Blas, Nayarit, Mexico.

The specimen had been obtained by members of an expedition to explore the western coast of North America captained by Frederick William Beechey on HMS Blossom.

Vigors coined the binomial name Pica colleriei, with the specific epithet chosen to honour Alexander Collie, the surgeon on board the Blossom, who had presented the specimen to the Zoological Society of London.

In juveniles, the crest has a white tip and the patch below the eye is smaller and darker blue than in adults.

[9] This species occurs in pairs or small groups in woodland, except for humid woodland, and partially open areas on the Pacific Slope of Mexico from southern Sonora south to Jalisco and northwestern Colima,[9] for a total of 160,000 km2 (62,000 sq mi).