The black-throated gray warbler was first described by John Kirk Townsend from a specimen collected near today's Portland, Oregon. It was known to the Chinook inhabitants of the northwest coast, who called it "Ah Kah a qual". Townsend described the species as "Sylvia nigrescens", placing it with the other New World warblers and the unrelated Old World warblers in the genus "Sylvia". It is now placed in the genus "Setophaga" along with about thirty other species, after having been classified in "Dendroica" for some time. Within its genus, it is part of a group with black throats and yellow face markings that includes the hermit warbler and Townsend's warbler. It is usually considered an early offshoot among this group of species, but genetic studies suggest a close relation to Grace's warbler.