Aphyodite tupebas can be diagnosed from other species of the genus Aphyodite by having only conical teeth in the premaxilla and dentary (vs. presence of tricuspid teeth in the premaxilla and dentary) and four longitudinal scale rows between the dorsal-fin origin and the lateral line (vs. five). It further differs from Aphyodite grammica by having 27-29 longitudinal scales (vs. 30-32); and from A. apiaka by having the sensory canal of the first infraorbital shorter than half length of bone (vs. sensorial canal of the first infraorbital longer than half length of bone) (Ref. 116757).