Molecular studies show the Black-headed Honeyeater is most closely related to the White-naped Honeyeater, and that their next closest relative is the Swan River Honeyeater.
The next closest relative outside the genus is the much larger but similarly marked Blue-faced Honeyeater.
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Treated as a subspecies of the White-naped Honeyeater for many years, it was found in a 2010 study to have diverged early on from the lunatus complex.
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It is a member of the genus Melithreptus with several species, of similar size and (apart from the Brown-headed Honeyeater) black-headed appearance, in the honeyeater family Meliphagidae.
Birds from southwestern Australia have been shown to be a distinct species, the Swan River Honeyeater, and the eastern birds more closely related to the Black-headed Honeyeater of Tasmania.
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