Traditionally treated as conspecific with Bolivian Brush-finch (Atlapetes rufinucha), but molecular-genetic studies indicate that the two are not even each other's closest relatives. It has been suggested that these two species, together with Vilcabamba Brush-finch (Atlapetes terborghi) and Black-faced Brush-finch (Atlapetes melanolaemus), and Slaty Brush-finch (Atlapetes schistaceus), are related in a complex manner, with yellow coloration lost or gained in a leap-frog pattern, such that taxa which do not look alike visually may in fact be closely related to each other. Vocal data and molecular studies suggest that subspecies nigrifrons may not belong with present species, is perhaps not even closely related to it, and possibly merits elevation to species rank; it should be noted that, when White-browed Brush-finch (Arremon torquatus) is placed in present genus, name nigrifrons becomes preoccupied and must then be replaced by name phelpsi.
Proposed subspecies simplex (described from Bogotá, and probably originating from eastern Andes of Colombia), appears indistinguishable from spodionotus and is synonymized with it.
The following 9 subspecies are recognised:
nigrifrons (Du Bus, 1855) - Perijá Mts, on northern Colombia-western Venezuela border. Considered by some authors to be a distinct species, Black-fronted Brush-finch (Atlapetes nigrifrons).
elaeoprorus (Sclater, PL & Salvin, 1879) - North-central Andes of Colombia in Antioquia.
yariguierum Donegan & Huertas, 2006 - Serranía de los Yariguíes (Santander), in Colombia.
caucae Chapman, 1927 - Western Andes and western slope at southern end of central Andes in Valle and Cauca, in Colombia.
spodionotus (Sclater, PL & Salvin, 1879) - Andes in southern Colombia (Nariño) and Ecuador (south to Chimborazo).
comptus (Sclater, PL & Salvin, 1879) - South-western Ecuador (from Cañar south to western Loja) and adjacent north-western Peru (Piura).
latinuchus (Du Bus, 1855) - South-eastern Ecuador (from eastern Azuay and eastern Loja) south to northern Peru (Amazonas).
chugurensis Chapman, 1927 - Pacific slope of Cajamarca, in north-western Peru.
baroni (Salvin, 1895) - Upper Marañón Valley in Cajamarca and La Libertad, in northern Peru.