The Erect-crested penguin is endemic only to the New Zealand Antipodes Islands and Bounty Islands. It is a crested penguin closely related to the extinct Chatham Island crested penguin, and is named after its upright yellow crests. The Erect-crested penguin breeds in large colonies on rocky terrain. Little is known about its biology and breeding habits. Populations have recently declined and the International Union for Conservation of Nature (IUCN) classifies it as endangered. The Erect-crested penguin is a Taonga, or treasured possession in Mori culture.We sequenced the genome of an adult Erect-crested penguin from Antipodes Island, New Zealand sub-Antarctic (provided by Chris Rickard/Sarah Fraser) to a depth of approximately 131x with short reads from a series of libraries with various insert sizes (250bp-20Kb). The assembled scaffolds of high quality sequences total 1.25Gb, with the contig and scaffold N50 values of 67.93Kb and 1.83Mb respectively. We identified 15786 protein-coding genes.