Yellow-crested Tanager is monotypic (Zimmer 1945, Dickinson and Christidis 2014, Clements et al. 2015). Further, genetic sampling within the range of this species (from Peru and Bolivia) has recovered only low levels of genetic divergence (0.6%; Burns and Racicot 2009).
Yellow-crested Tanager belongs to the subfamily known as the Ornamented Tanagers (Tachyphoninae), which are named for their social ornaments such as colorful crests and other small bright patches of high contrast; the Ornamented Tanagers consists of 31 species mostly belonging to the genera Tachyphonus and Ramphocelus (Burns et al. 2014).
Molecular phylogenetics consistently has recovered a paraphyletic Tachyphonus (Burns and Racicot 2009, Burns et al. 2014). The type species of Tachyphonus is White-lined Tanager (T. rufus), yet this species is distantly related to Yellow-crested Tanager (Burns and Racicot 2009, Burns et al. 2014). Yellow-crested Tanager is sister to Flame-crested Tanager (T. cristatus), and these two species likely diverged due to allopatric speciation along the Amazon River and the Fitzcarrald Arch (Hayes and Sewlal 2004, Burns and Racicot 2009). The clade formed by these two species is in turn sister to White-shouldered Tanager (T. luctuosus), and this group of three species of "Tachyphonus" have recently been proposed to be moved to the new genus Islerothraupis (Burns et al. 2014, Burns et al. 2016). This suggests that the loss of the manubrium-sternum bridge in some members of Tachyphonus sensu lato has evolved multiple times (Webster 1992). Islerothraupis is sister to a clade formed by Black-goggled Tanager (Trichothraupis melanops) and Gray-headed Tanager (Eucometis penicillata), which despite superficially different appearances, share crested males and brightly colored patches of carotenoid-bearing plumage (Burns et al. 2014).
Tachyphonus rufiventer was described as Tanagra rufiventer (Spix 1825) from São Paulo do Olivença, Rio Solimões, Brazil (Hellmayr 1920, Storer 1970). Synonyms include Tachyphonus serrirostris Stone 1899 and Tachyphonus metallactus (Oberholser 1919, e.g., Hellmayr 1936, Bond and Meyer de Schauensee 1942, Pinto 1944), as listed in Storer (1970) and Remsen et al. (SACC Version: 7 August 2016), but see Zimmer (1945) and Meyer de Schauensee (1966); both were synonymized with T. rufiventer by Bond (1955). The discovery of a paraphyletic Tachyphonus initially led to the suggestion for merging all species in this larger clade (including all Tachyphonus sensu lato and Ramphocelus) into the genus Lanio (Burns and Racicot 2009), and "Lanio rufiventer" subsequently was adopted by some authorities (e.g., CBRO 2010), but ultimately rejected for a many-genera alternative (Burns et al. 2014).