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The blue penguins (genus Eudyptula) have been subjected to extensive taxonomic revision. In 1976, the genus was reduced from 2 species to a single species (Eudyptula minor) with 6 subspecies, based on a morphometric analysis. Despite the later proposed rejection of the differentiation of subspecies in Eudyptula minor, following analysis of allozymes in some populations, the 6 subspecies have continued to be recognised in some popular and scientific literature. We compared the sequences of 3 mitochondrial gene regions (small ribosomal subunit, cytochrome oxidase b and the control region) from the 6 hypothesised subspecies to examine relationships within Eudyptula. We found evidence for 2 unexpected clades: the 1st consisting of Otago and Australian populations, the 2nd consisting of north- ern, Cook Strait, Chatham Island, and Banks Peninsula populations. Some support for these 2 clades was also found from a re-analysis of morphometric data and from a preliminary examination of vocalisations.