分子時計
Molecular clock evidence using DNA suggests the macaroni penguin split from its closest relative, the royal penguin ("Eudyptes schlegeli"), around 1.5 million years ago. The two have generally been considered separate species, but the close similarities of their DNA sequences has led some, such as the Australian ornithologists Les Christidis and Walter Boles, to treat the royal as a subspecies of the macaroni. The two species are very similar in appearance; the royal penguin has a white face instead of the usually black face of the macaroni. Interbreeding with the Indo-Pacific subspecies of the southern rockhopper penguin ("E. chrysocome filholi") has been reported at Heard and Marion Islands, with three hybrids recorded there by a 1987–88 Australian National Antarctic Research Expedition.