Aracajuia was placed in the Family Cytheruridae Mller by Musacchio and Simeoni (2008), with no further systematic details. However, it is here classified in the Family Cytheridae, Subfamily Schizocytherinae, based on the presence of a distinctive schizodont hinge in the type-species, Aracajuia benderi, which characterizes this group. The original diagnosis was emended for simplicity so that the diagnostic features would be more identifiable. Some of the original features were removed from the diagnosis (shape of lateral and marginal pore canals; structures of the marginal zone, such as the inner margin and concrescence line; and taxonomic ranking), while others were incorporated (the central muscle scar pattern). Aracajuia is considered a valid genus, distinguished mainly by the position of the three ridges along the lateral surface of the carapace and by its sexual dimorphism. Musacchio and Simeoni (2008) described Aracajuia as entomodont, but examination of the individuals from sample MP-291 shows that it clearly is not; these authors also stated that Acrocythere Neale resembles Aracajuia but has a different hinge. According to the original diagnosis, the hinge of Acrocythere is entomodont as for Orthonotacythere (Alexander, 1933; Neale, 1960). Aracajuia could be derived from Acrocythere, which would explain their similarities, but also the greater complexity of the former's hinge. Fissocarinocythere Brouwers and Hazel is comparable to Aracajuia, but the two genera can be separated by their outline in dorsal view and by the ornamentation of the anterior end (smooth in Fissocarinocythere and ridged in Aracajuia). The similarity between Aracajuia and Sondagella was first noted by Dingle (1999), and the synonymy was employed by Musacchio and Simeoni (2008) and Ruault-Djerrab and Kechid-Benkherouf (2011). Some authors (Ballent, 2009; Ballent andWhatley, 2009; Concheyro et al., 2009) continued to recognize Sondagella as a valid genus, based on Bate (1972), despite previous discussion. Species originally attributed to Sondagella present the diagnostic characteristics described above for Aracajuia overall carapace shape, lateral surface ornamentation, especially the morphology of the three main ridges, hinge type and sexual dimorphism; therefore, Sondagella is here considered to be a junior synonym of Aracajuia. The present authors assign several species previously identified as Amphicytherura or Sondagella to Aracajuia, as detailed in Table 1.

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Aracajuia was named by Krömmelbein (1967) [Antonietto et al. (2013) age data: Jurassic(?)-Cretaceous, Tithonian(?)-Santonian. Reference number: 64785.]. Its type is Aracajuia benderi.

It was assigned to Trachyleberididae by Ceolin et al. (2024).