Aphyodite apiaka is distinguished from other species of the genus Aphyodite by the length of the sensory canal of the first infraorbital bone, which is longer than half length of bone (vs. shorter than half length of bone). It further differs from Aphyodite grammica by having 26 to 28 longitudinal scales (vs. 30 to 32), 7 or 8 predorsal scales (vs. 9 or 10), 11 to 13 dentary teeth (vs. 14 to 16), and i12 pectoral rays (vs. i10 or i11); and from A. tupebas by having tricuspid teeth in the premaxilla and dentary (vs. only conical teeth in the premaxilla and dentary), and by having five longitudinal scale rows between dorsal-fin origin and lateral line (vs. four) (Ref. 116757).