Blue penguins, Eudyptula minor, breeding on Penguin Island, Western Australia are considerably larger than other blue penguins in Australia. If genetic isolation is the cause, it may have implications for the conservation status of some blue penguin populations. We compared the sequences of two mitochondrial gene regions (cytochrome‐b and the control region) from Western Australian blue penguins with other populations of blue penguins from Australia and New Zealand. We found few differences between sequences from Western Australia, Phillip Island, Victoria and Otago, New Zealand, although all three differed considerably from other New Zealand blue penguins. Sequences for the control region from the Western Australian blue penguins and 30 more birds breeding at various Australasian sites provided further support for two major clades within Eudyptula; an Australian clade (including Otago) and a New Zealand clade.