Two subspecies have been recognized: Ramphocelus flammigerus flammigerus and Ramphocelus flammigerus icteronotus (Dickinson and Christidis 2014, Clements et al. 2015).
The two subspecies of R. flammigerus have different geographical distributions (Meyer de Schauensee 1966).
R. f. flammigerus is only present in western Colombia: upper tropical and subtropical zone of the Pacific slope, from the upper Rio San Juan southward to Narino and eastward into the middle Cauca Valley (Clements and Shany 2001). For description of the plumage of this subspecies, see Detailed Description (Appearance).
R .f. icteronotus is more widely distributed and conspicuous from Panama and western Colombia to a small region of northwestern Peru: eastern Bocas del Toro east through San Blas, El Valle and from Canal Zone area east through humid lowlands of eastern Panama province and Darien (Restall et al. 2007). Thus, R. f. icteronotus occupies Ecuador in addition to Colombia and Peru (Meyer de Schauensee 1966). This subspecies is commonly known as the Lemon-rumped or Yellow-rumped Tanager because both male and female have a bright yellow lower back and rump; otherwise this subspecies is very similar to the nominate subspecies. However, the female has grayish brown above, pale yellow below for the most part and whitish throat (Meyer de Schauensee 1966).
On the west slope of the Andes, in the upper Rio San Juan region, the two subspecies interbreed with each other (Ridgely and Tudor 1994).
Ramphocelus flammigerus is in the tanager family Thraupidae and belongs to the subfamily Tachyphoninae (Burns et al. 2014). This subfamily, also known as the ‘ornamented tanagers’, includes many species distributed across the Neotropical lowlands, and most species have social ornaments such as crests or bright color patches (Burns et al. 2014). There are 10 genera (including Ramphocelus) in this subfamily. The genus Ramphocelus includes nine species and is most closely related to a clade containing three Tachyphonus species (T. phoenicius, T. coronatus, and T. rufus; Burns et al. 2014). Ramphocelus flammigerus forms a superspecies with R. passerinii and R. costaricensis (Paynter and Storer 1970). DNA evidence (Burns and Racicot 2009, Burns et al. 2014) indicate that these three species form a monophyletic group. Ramphocelus flammigerus shows 4.7% sequence divergence from R. passerinii and R. costaricensis, which indicates a long period of isolation of R. flammigerus from the other two species (Burns et al. 2014). Burns and Racicot (2009) included two individuals of R. flammigerus in their study, one from Panama and one from Ecuador. Both individuals represent the icteronotus subspecies group. These two individuals showed 2.2% sequence divergence, a moderately high level of divergence within bird species (Burns and Racicot 2009). The Central American distributions of species within Tachyphoninae are mostly the result of multiple dispersal events into Central America from South America (Burns and Racicot 2009). However, the distribution of R. flammigerus may instead involve a dispersal event from Central America to South America (Burns and Racicot 2009).