The Ruby-crowned Tanager does not have any subspecies; it is monotypic (Dickinson and Christidis 2014, Clements et al. 2015). Further, genetic sampling from distant parts within the range of the Ruby-crowned Tanager have found only shallow (0.8%) mitochondrial sequence divergence (Burns and Racicot 2009).
The Ruby-crowned Tanager, Tachyphonus coronatus (Vieillot, 1822), was described as Agelaius coronatus by Vieillot based on Tordo de Bosque Coronado y Negro (Bonnaterre and Vieillot 1802), with a type locality of Páxaros, Paraguay (Storer 1970, Hilty 2011). Within T. coronatus, analysis of 50 individuals sequenced for cytB recovered two populations, though there was little differentiation between these populations (Cabenne et al. 2016). The genus Tachyphonus has regularly been recovered as paraphyletic by molecular phylogenetic analyses (e.g., Burns and Racicot 2009, Burns et al. 2014). As such, many species formally considered Tachyphonus have been assigned to new genera (Burns et al. 2016). However, the Ruby-crowned Tanager is sister to the White-lined Tanager (T. rufus), which is the type species for the genus Tachyphonus. The clade formed by these two species are sister to the Red-shouldered Tanager (T. phoenicius), and these three species will likely keep their current generic name (Burns et al. 2014, Burns et al. 2016). The Red-shouldered Tanager lineage spilt from this sister clade approximately 11.7 MYA (Matos et al. 2016). These three Tachyphonus species are in turn sister to the monophyletic Ramphocelus tanagers (Burns et al. 2014). This clade is contained in a larger group known as the Ornamented Tangers, or the Tachyphoninae, which includes all current and previous members of the genus Tachyphonus, as well as Lanio and other species of tanagers that tend to be ornamented with highly-contrasting crests, epaulettes, rump patches, etc. - thus the Ornamented Tanagers (Burns et al. 2014). Ruby-crowned Tanagers have hybridized with the Brazilian Tanager (Ramphocelus bresilius) in captivity (Sick 1993).