Two indigenous bat species have been identified as present in, or near, Otago: the pekapeka-tou-roa or the long-tailed bat (Chalinolobus tuberculatus) and the pekapeka-tou-poto or the southern lesser short-tailed bat (Mystacina tuberculata tuberculata).

Our bats are nocturnal (active at night) and use very high-pitched sounds (called echo-location that is mostly above the range of human hearing) to navigate. The sounds they make are reflected back, and they use these reflections to locate and avoid objects in their path and to hunt.

Our bats also have small bodies and relatively large wings, perfect for squeezing many bats into a roost and for flying in forests. Unusually for bats, the lesser short-tailed bat is also agile on the ground, often foraging for food on the forest floor by using its folded wings as limbs.

A third indigenous bat species is regionally extinct, the greater short-tailed bat (Mystacina robusta).

The greater short-tailed bat and lesser short-tailed bat are the only remaining examples of the Mystacina family of bats in the world.

Māori folklore refer to bats as pekapeka and associate them with the mythical, night-flying bird, hōikioi, which foretells death or disaster.

In a regional threat assessment, the pekapeka-tou-roa or the long-tailed bat was identified as Regionally Critical, the most severely threatened status, and the pekapeka-tou-poto or the southern lesser short-tailed bat as Regionally Data Deficient, due to information lacking so that an assessment was not possible.

The greater short-tailed bat was identified as Regionally Extinct, because this species has not been seen since 1967, with this happening outside Otago.