Two subspecies distinct from the nominate form have been described based on limited material (van Rossem 1934, Hellmayr and Conover 1942, Ridgway and Friedman 1946), resulting in three subspecies: nominate Penelopina nigra nigra in Mexico, Guatemala, and southwestern El Salvador; P. n. dickeyi in El Salvador and Honduras; and P. n. rufescens in Nicaragua. Examination of larger series revealed no geographic variation and no constancy of the subtle morphological subspecies characters (color of gloss, color of eye ring) used by van Rossem (Vaurie 1967). Therefore all subspecies now are considered synonyms of nominate Penelopina nigra (Vaurie 1967, Dickinson 2003, Clements et al. 2011).
Highland Guan belongs to the family Cracidae (curassows, guans, and chachalacas), which is placed in the order Galliformes together with the families of megapodes (Megapodiidae), turkeys (Melaegrididae), grouse (Tetraonidae), New World quails (Odontophoridae), pheasants and partridges (Phasianidae), and guineafowl (Numididae) (del Hoyo 1994). Highland Guan was originally described as Penelope niger (Fraser 1850). The monotypic genus Penelopina was established by Reichenbach (1862). Penelopina differs in some unique characters from other members of the subfamily Penelopinae, such as a distinct juvenile male plumage and females being larger than males (Vaurie 1968).
Traditionally, the family Cracidae is divided into two subfamilies, Cracinae and Penelopinae, based on morphological differences of the pelvic bone (Huxley 1868, Ridgway and Friedmann 1946, del Hoyo 1994, Dickinson 2003). Penelopina has been grouped together with the genera Ortalis, Penelope, Pipile, Aburria, Chamaepetes, and Oreophasis in the latter subfamily, and the genera Crax, Nothocrax, Mitu, and Pauxi in the Cracinae.
This division, however, has been controversial. Based on morphological characters, Sclater and Salvin (1870) divided the Cracidae in three subfamilies by establishing the additional subfamily Oreophasinae for Oreophasis. Vaurie (1968) agreed on the special position of Oreophasis and suggested three tribes Penelopini, Oreophasini, and Cracini. Vuilleumier (1965) and AOU (1998) did not recognize subfamilies.
Based on mitochondrial segments and nuclear genes, Pereira et al. (2002) identified four clades in the family Cracidae: curassows (Mitu, Pauxi, Nothocrax, and Crax), Horned Guan (Oreophasis), chachalacas (Ortalis), and guans (Aburria, Pipile, Penelope, Chamaepetes, and Penelopina). In this analysis, Penelopina was closely related to Chamaepetes. A cladistic study combining molecular (mitochondrial genes), morphological, and behavioral characters (Frank-Hoeflich et al. 2007) resulted in Penelopina as a sister group of Penelope, Pipile, and Aburria. These four genera are a sister group to Chamaepetes. These five genera are a sister group to Ortalis, and all of these genera form the subfamily Penelopinae. Oreophasis resulted as a sister lineage to the other genera of Cracinae (Nothocrax, Pauxi, Mitu, and Crax).