Described by Cabanis in 1860 as Compsothlypis gutturalis, with type locality Irazú, Costa Rica. Ridgway (1884) established the genus Oreothlypis for gutturalis and for superciliosa (Crescent-chested Warber), and continued to use this name for both species (e.g. Ridgway 1902). Most subsequent authors, however, variably classified the Flame-throated Warbler in the genus Vermivora (e.g., Hellmayr 1935, Lowery and Monroe 1968) or in the genus Parula (e.g., American Ornithologists' Union 1983, 1998).
Sangster (2008) reviewed recent literature on the phylogenetic relationships of parulid genera, with particular reference to Vermivora. As he pointed out, a variety of genetic phylogenetic studies (using approaches that included starch gel electrophoresis and DNA sequencing) demonstrated that the genus Vermivora is polyphyletic, that gutturalis and superciliosa are sister species, and that gutturalis + superciliosa are sister in turn to a large clade of species traditionally classified as Vermivora. The oldest available generic name for this clade is Oreothlypis (Sangster 2008).