Yellow-eyed penguins (YEPs) have suffered major population declines over the past 30 years, with no single cause established. Leucocytozoon was first identified in yellow-eyed penguins in 2005. During the 2008/09 breeding season, a high mortality was seen in both mainland yellow-eyed penguins as well as those on Enderby Island of the Auckland Islands archipelago. A high overall prevalence of Leucocytozoon spp. in association with a high incidence of chick mortality was observed during this period on Enderby Island. One chick had histological evidence of leucocytozoonosis with megaloschizonts in multiple organs throughout its body. In addition, a high prevalence (73·7%) of Leucocytozoon was observed by PCR in the blood of adult Enderby yellow-eyed penguins taken during the 2006/07 season. These findings were different from the low prevalence detected by PCR on the coast of the South Island (11%) during the 2008/2009 breeding session and earlier on Campbell Island (21%) during the 2006/2007 breeding session. The Leucocytozoon spp. sequences detected lead us to conclude that the Leucocytozoon parasite is common in yellow-eyed penguins and has a higher prevalence in penguins from Enderby Island than those from Campbell Island and the mainland of New Zealand. The Enderby Island yellow-eyed penguins are infected with a Leucocytozoon spp. that is genetically distinct from that found in other yellow-eyed penguin populations. The role of Leucocytozoon in the high levels of chick mortality in the yellow-eyed penguins remains unclear.