Before 2016, authors had recognized between 11 and 13 subspecies (sometimes called races).

A
2016 molecular study revised that to nine subspecies, made two others their own species (P. nanus
—Darwin's flycatcher, P. dubius—San Cristóbal flycatcher, P. rubinus—scarlet flycatcher), and
determined that another was not valid (P. major). Some works still refer to the vermilion flycatcher
as Pyrocephalus rubinus, which can lead to confusion with the scarlet flycatcher (also
called Pyrocephalus rubinus).[8][9][12] The vermilion flycatcher likely evolved around 1.15 million years
ago (mya), the species on the Galápagos Islands having split off around 0.82 mya. The South
American subspecies had coalesced by about 0.56 mya, and the North American subspecies had
diverged from the South American by 0.25 mya.[8]
There are nine widely recognized subspecies, which differ primarily in the color and saturation of the
male's plumage and the color and amount of streaking of the female's. The geographic boundaries
between some subspecies are not well defined:[9]

 P. o. obscurus (Gould, 1839)—The nominate race, which is found in the Lima region of

western Peru.[9]
 P. o. mexicanus (Sclater, 1859)—Found from southern Texas in the United States south to
central and southern Mexico.[9] Its upperparts are the blackest of any race, and the male lacks
any mottling on the red parts.[2] This subspecies is named after Mexico.[11]:252
 P. o. saturatus (von Berlepsch and Hartert, 1902)—Found in northeastern Colombia, western and
northern Venezuela, Guyana and northern Brazil. [9] The female has pink underparts.
[2]
 Saturatus means "richly colored" in Latin. [11]:54
 P. o. blatteus (Bangs in 1911)—Found in southeastern Mexico, Belize and northern
Guatemala.[9] The upperparts are paler, and the underparts more red compared to the nominate
race, lacking an orange tinge. It is also smaller than the other Mexican races. [2] Blatteus means
"purple colored" in Latin.[11]:73
 P. o. flammeus (van Rossem, 1934)—Found in the southwestern United States and
northwestern Mexico.[9] The upperparts are paler and slightly gray, and the underparts are more
orange colored than the nominate race. Males may also have orange mottling in the crown and
breast, whereas the females are less streaky.[2] Flammeus means "flame colored" in Latin.[11]:54
 P. o. ardens (Zimmer, 1941)—Found in northern Peru, in extreme
eastern Piura, Cajamarca and Amazonas.[9] Their coloration has been described as "fiery red".
The front of the females crown is slightly pink.[2] Ardens means "burning" in Latin.[11]:54
 P. o. cocachacrae (Zimmer, 1941)—Found from southwestern Peru south to extreme northern
Chile.[9] The male has a browner mantle and less red underparts, while the female has less white
underparts, compared to the nominate race. The type locality is the Cocachacra District in Peru.
[2]

 P. o. piurae (Zimmer, 1941)—Found from western Colombia south to northwestern Peru, it is

named for the Piura province in Peru.[9][11]:309
 P. o. pinicola (Howell, 1965)—Found in eastern Honduras and northeastern Nicaragua. [9] It is
smaller than P. o. blatteus, and the females have more orange underparts. It
prefers pine savanna habitats, which is reflected in the name Pinicola: it roughly translates to
"pine tree dweller" from Latin. [2][11]:307