Geographic variation in the colour pattern of Phainoptila melanoxantha indicates the existence of two well-defined forms. P. m. melanoxantha corresponding to the populations of the Talamanca range and the Central Volcanic range and P. m. parkeri corresponding to the populations that inhabit the Tilarán and the Guanacaste ranges (Barrantes & Sánchez, 2000). This form differs from populations of the Corrdilleras de Talamanca and Volcanica Central by its completely yellow belly in males (as opposed to grey), and its shorter wing and also its tails and in females, the streaked pattern of the breast.
The taxonomic lineage of Phainoptila have long been controversial, since so little is known of the bird (Wolf, 1976). In fact, the genera Phainoptila, Ptiliogonys and Phainopepla are usually treated as a single family: Ptiliogonatidae (Wetmore, 1960), but also as a subfamily of the waxwing family Bombycillidae (Greenway, 1960). Other authors consider these classifications as tentative or unproved, recognizing separate families for some of these groups (Spellman et al., 2008). However, they seem to be related to members from the Turdidae family. For example, with Myadestes, by a taxonomic history and egg-white protein relation study (Sibley, 1973).