The nanday parakeet was previously regarded as a member of the monotypic genus "Nandayus" Bonaparte, 1854 one of the rough 16 genera of Neotropical parrots of tribe Arini which includes the conures and macaws. However, phylogenetic evidence showed that it is positioned in one of the four groups in the genus "Aratinga". When the genus "Aratinga" was revised and split in four separate genera, this species was included in the current genus "Aratinga". This revision was based on earlier studies. According to a mtDNA-based phylogenetic analysis of the genus "Aratinga" by Ribas & Miyaki (2004), the nanday conure forms a monophyletic group with the sun conure ("A. solstitialis"), jenday conure ("A. jandaya"), and golden-capped conure ("A. auricapilla"). Tavares "et al." (2005) in a mitochondrial and nuclear DNA analysis of 29 species representing 25 of 30 genera of Neotropical parrots found the nanday conure's closest relative to be "Aratinga solstitialis", the sun conure, and the time of divergence of the species to have been 0.5 to 1.3 Mya.