Two subspecies of T. melanocephalus have been described: nominate T. m. melanocephalus [Gould 1836], found on the eastern slopes of Central America from Mexico to northeastern Costa Rica; and T. m. illaetabilis [Bangs 1909], found in western Costa Rica and Nicaragua. The latter was described by O. Bangs from a type specimen collected in Bolson, Costa Rica, December 25, 1907, by C. F. Underwood (collection of E. A. and O. Bangs no. 22781; type now in the Museum of Comparative Zoology [Bangs 1930]). Described as similar to T. m. melanocephalus "except that adult male has head, throat, and chest dark gray-slate color to blackish slate, instead of black; the adult female with these parts and the back and scapulars also, much paler and grayer than in true T. melanocephalus. Size averaging slightly larger and the bill slightly heavier" (Bangs 1909; see Measurements.) Bangs (1909) noted that juveniles of both subspecies are duller than adults, but indicated that juveniles of the two subspecies were nevertheless easily distinguishable. T. m. illaetabilis also referred to as "slaty-headed trogon" (Latin name denotes "joyless" or "cheerless").
The ranges of the two subspecies are not completely disjunct, overlapping in central Nicaragua and northern Costa Rica (note that this range overlap is not shown on the distribution map in Johnsgard ). The taxonomic status of individuals in this part of the range is not clear. Geographic variation in vocalizations has not been studied and recordings of the two subspecies are not noticeably different (see Vocalizations).
Trogon melanocephalus Gould . Trogoniformes: Trogonidae. The trogons and quetzals form a monophyletic group with distinctive, conserved morphology and a pan-tropical distribution. The New World genus Trogon is the largest of the six genera in the family, containing 21 species recognized by the AOU (2012). The phylogenetic placement of Trogon in relation to other genera currently is debated. Based on mitochondrial cytochrome b and 12S ribosomal RNA sequence data, Espinosa de los Monteros (1998) placed Trogon in a clade with other New World genera (Euptilotus, Pharomachrus, and Priotelus) with the Asian genus Harpactes being sister to this clade and the African genus Apaloderma being, in turn, the basal group. By contrast, Moyle (2005) used nuclear and mitochondrial sequence data to place Trogon in a clade with the Old World Harpactes and Apaloderma, with Priotelus being sister to this clade and Euptilotus and Pharomachrus forming the basal group. In this analysis, the estimated time of divergence of Trogon from the Old World trogons was 23.8 million years ago (range 17.8 – 35.3 mya).
Trogon melanocephalus is closely related to the allopatric Citreoline Trogon (T. citreolus), which is found in more arid habitats on the Pacific coast of Mexico. T. melanocephalus was considered to be a subspecies of T. citreolus by Peters (1945), and some older accounts refer to T. melanocephalus as "Black-headed Citreoline Trogon" (e.g. Skutch 1948, Foster 1975). More recent taxonomic accounts treat the two taxa as separate, recently diverged species that together form a superspecies (Sibley and Monroe 1990, Clements et al. 2011, AOU 2012). Separation of T. melanocephalus from T. citreolus is supported by allopatric distribution, consistent phenotypic differences, and molecular analysis (Moyle 2005, Da Costa and Klicka 2008, Orneras et al. 2009). The extent of secondary contact between the two populations is not known; the most likely area of overlap is on either side of the continental divide in Oaxaca and Chiapas states, Mexico, with the possible contact zone running approximately east-west between Oaxaca and Tuxtla Gutiérrez. At least one specimen has been reported from this area that shows phenotypic traits of both melanocephalus and citreolus, indicating possible hybridization (Schaldach et al. 1997; see Similar Species).
The T. melanocephalus-citreolus clade is sister to the clade containing T. viridis (Green-backed Trogon), T. chironurus (White-tailed Trogon), and T. bairdii (Baird's Trogon). Morphologically, these taxa all have gray-backed females, blue-headed males, and contrasting black and white tail patterns.
Two subspecies of T. melanocephalus have been recognized: T. m. melanocephalus of Mexico and eastern Central America, and T. m. illaetabilis of western Central America (see Geographic Variation).
Gould (1836) described the species from a type specimen collected in Tamaulipas, Mexico and stated that the type "is now in the collection of the Zoological Society of London". Stresemann (1954) listed as types two specimens collected from Valle Nacional (Oaxaca) and Alvarado (Veracruz) by Ferdinand Deppe in 1826, housed in the Berlin Museum; however, the designation of these as types is probably in error (Binford 1990). Other historical specimen records include a female collected from Tigré Island, Honduras, 1858, by G. C. Taylor and other records contained in Ridgway (1911).