The Fiordland crested penguin (also known as Fiordland penguin, and in Mori it is known as Tawaki) is endemic only to the south-western coasts of New Zealand's South Island as well as on Stewart Island/Rakiura and nearby islands. It is a crested penguin closely related to the Snares crested penguin. Historically, Fiordland crested and Snares crested penguins were considered incipient - however can be distinguished from the Snares crested penguin by having no bare skin around the base of its bill. The Fiordland crested penguin breeds among tree roots and rocks in dense temperate coastal forest, laying a clutch of two eggs where the first-laid egg is much smaller than the second egg, and generally hatches later, with higher mortality. This breeding system demonstrates a brood reduction system that is unique from other avian groups. The Fiordland crested penguin was probably more widely distributed before human arrival to New Zealand ~750 years ago. The International Union for Conservation of Nature (IUCN) classifies the Fiordland crested penguin as vulnerable, and the New Zealand Department of Conservation classifies them as endangered. The Fiordland crested penguin is a Taonga, or treasured possession in Mori culture.We sequenced the genome of an adult Fiordland-crested penguin from Harrison Cove, Milford Sound, New Zealand South Island (provided by Thomas Mattern/Theresa Cole) to a depth of approximately 115x with short reads from a series of libraries with various insert sizes (250bp-20Kb). The assembled scaffolds of high quality sequences total 1.17Gb, with the contig and scaffold N50 values of 32.54Kb and 8.39Mb respectively. We identified 19170 protein-coding genes.