The lithobiomorph centipede Henicops is widely distributed in Australia and New Zealand, with five described species, as well as two species in New Caledonia and Lord Howe Island. Parsimony, maximum likelihood and Bayesian analyses of ca. 800 aligned bases of sequence data from 16S rRNA and 28S rRNA were conducted on a dataset including multiple individuals of Henicops species from populations sampled from different parts of species' geographic ranges, together with the allied henicopines Lamyctes and Easonobius. Morphological characters are included in parsimony analyses. Molecular and combined datasets unite species from eastern Australia and New Zealand to the exclusion of species from Western Australia, New Caledonia and Lord Howe Island. The molecular data favour these two geographic groupings as clades, whereas inclusion of morphology resolves New Caledonia, Lord Howe Island, southwest Western Australia and Queensland as successive sisters to southeastern Australia and New Zealand. The basal position of the Lord Howe Island species in the phylogeny favours a diversification of Australasian Henicops since the late Miocene unless the Lord Howe species originated in a biota that pre-dates the island. The molecular and combined data resolve the widespread morphospecies H. maculatus as paraphyletic, with its populations contributing to the geographic groupings New South Wales + New Zealand and Tasmania + Victoria.