The Snares crested penguin (also known as Snares penguin, Snares Islands penguin, and in Māori it is known as pokotiwha) is endemic only to the New Zealand Snares Islands and Western Chain. It is a crested penguin closely related to the Fiordland crested penguin. Historically, Snares crested and Fiordland crested penguins were considered incipient - however the Snares crested penguin can be distinguished from the Fiordland crested penguin by having bare skin around the base of its bill. The Snares crested penguin breeds among tree roots and rocks in dense forest or in the open, laying two eggs, the second of which is larger and hatches first rather than being the smallest and last to hatch. The International Union for Conservation of Nature (IUCN) classifies the Snares crested penguin as vulnerable. The Snares crested penguin is a Taonga, or treasured possession in Māori culture.We sequenced the genome of an adult Snares-crested penguin from Dunedin Wildlife Hospital, originally from The Snares, New Zealand sub-Antarctic (provided by David Thompson) to a depth of approximately 138x with short reads from a series of libraries with various insert sizes (250bp-20Kb). The assembled scaffolds of high quality sequences total 1.15Gb, with the contig and scaffold N50 values of 29.02Kb and 0.35Mb respectively. We identified 17126 protein-coding genes.