Describing geographic variation for this species depends on whether the Beautiful Woodpecker (M. pulcher) is considered a separate species or a subspecies of M. chrysauchen (see Systematics below). M. pulcher differs from M. chrysauchen: (1) white on mantle is partly barred, (2) paler forehead patch extends to forecrown, (4) belly more extensively barred, and (5) red crown of male extends all the way to the nape. The females differ more; in chrysauchen, the crown is mostly yellowish with a narrow transverse black band, whereas in pulcher, the forehead is whitish, most of the crown in black, and the hindcrown is red, with yellowish only on the nape plumage (Winkler and Christie 2002).
Melanerpes is one of the genera in the subfamily Picinae, one of three subfamilies within the family Picidae (Webb and Moore 2005, American Ornithologists' Union 1998). Composition within the genus has changed over the years. Golden-naped Woodpecker was described in 1870 as Melanerpes chrysauchen (Salvin 1870), with a type locality of Bogaba [Chiriquí], Panama; subsequently chrysauchen was moved to the genus Tripsurus (Ridgway 1914) and later merged back into Melanerpes (Peters 1948).
Short (1982) considered chrysauchen to be a member of a superspecies that also included Melanerpes cruentatus (Yellow-tufted Woodpecker), Melanerpes flavifrons (Yellow-fronted Woodpecker), and Melanerpes pucherani (Black-cheeked Woodpecker). Most authors treat chrysauchen as monotypic (e.g, Ridgway 1914, Cory 1919, Wetmore 1968, Stiles and Skutch 1989, Remsen et al. 2012), but Short (1982) and Winkler and Christie (2002) include Melanerpes pulcher (Beautiful Woodpecker) as a subspecies of chrysauchen; see Geographic Variation.