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We investigated diversity and community composition of microarthropods (Collembola and Oribatida) in a range of habitats in the high alpine zone of New Zealand’s South Island. We report the first comprehensive record of the fauna for the high alpine zone, and discuss habitat associations and related changes in community composition. A total of 51 species of Collembola and 70 species of Oribatida were collected. The microarthropod communities in alpine New Zealand had some structural traits in common with arcto-montane environments elsewhere in the world, but were not completely comparable. There was a minimal similarity between the faunal complexes of Oribatida and Collembola in alpine habitats and the known fauna of New Zealand, with high proportion of species new to science.