Often considered a subspecies of Yellow-breasted Brush-finch (Atlapetes latinuchus), and both were originally considered part of a wider complex that included also Vilcabamba Brush-finch (Atlapetes terborghi) and Bolivian Brush-finch (Atlapetes rufinucha), although recent studies suggest that various components of this group may not be each other's closest relatives. Present species likely closest to Vilcabamba Brush-finch (Atlapetes terborghi). One specimen of nominate subspecies of Bolivian Brush-finch (Atlapetes rufinucha) from La Paz (Bolivia) exhibits dark scalloping on breast, approaching present species. It is unclear if this is a variation in former species or due to gene flow between the two.