Colonies on the Otago Peninsula are a popular tourist venue, where visitors may closely observe penguins from hides, trenches, or tunnels.

On the Otago Peninsula, numbers have dropped by 75% since the mid-1990s and population trends indicate the possibility of local extinction in the next 20 to 40 years.

While the effect of rising ocean temperatures is still being studied, an infectious outbreak in the mid-2000s played a large role in the drop.

Human activities at sea (fisheries, pollution) may have an equal if not greater influence on the species' downward trend.

Mitochondrial and nuclear DNA evidence suggests it split from the ancestors of Eudyptes around 15 million years ago.

The yellow-eyed penguin (M. a. antipodes) is most easily identified by the band of pale yellow feathers surrounding its eyes and encircling the back of its head.

Males are generally longer lived than females, leading to a sex ratio of 2:1 around the age of 10–12 years.

However, genetic analysis has since revealed that its range only expanded to include mainland New Zealand in the past 200 years.

[28] There is little gene flow between the northern and southern populations as the large stretch of ocean between the South Island and subantarctic region and the subtropical convergence act as a natural barrier.

[30] Whether yellow-eyed penguins are colonial nesters has been an ongoing point of debate among zoologists in New Zealand.

After the chicks are six weeks of age, both parents go to sea to supply food to their rapidly growing offspring.

Around 90% of the yellow-eyed penguin's diet is made up of fish, chiefly demersal species that live near the seafloor, including silversides (Argentina elongata), blue cod (Parapercis colias), red cod (Pseudophycis bachus), and opalfish (Hemerocoetes monopterygius).

[33][34] Other species taken are New Zealand blueback sprat (Sprattus antipodum) and cephalopods such as arrow squid (Nototodarus sloanii).

[43] A reserve protecting more than 10% of the mainland population was established at Long Point in the Catlins in November 2007 by the Department of Conservation and the Yellow-eyed Penguin Trust.

[49] Several mainland habitats have hides and are relatively accessible for those wishing to watch the birds come ashore.

In addition, commercial tourist operations on Otago Peninsula also provide hides to view yellow-eyed penguins.

[50] Studies have shown however, that human presence in their habitats negatively impacts their foraging and breeding habits.