This is a list of mammals in Indonesia. It is derived from the IUCN Red List and includes those mammals that have been extinct since 1500. The following tags are used to highlight each species' conservation status:

Subclass: Yinotheria

Order: Monotremata (monotremes)

Monotremes are mammals that lay eggs instead of giving birth to live young. Momotremata comprises the platypus and echidnas.

Subclass Metatheria

Order: Dasyuromorphia (carnivorous marsupials)

The order Dasyuromorphia comprises most of the carnivorous marsupials, including quolls, dunnarts, the numbat, the Tasmanian devil, and the recently extinct thylacine.

Order: Peramelemorphia (bandicoots and bilbies)

Peramelemorphia includes the bandicoots and bilbies: it equates approximately to the mainstream of marsupial omnivores. All members of the order are endemic to the twin land masses of Australia-New Guinea and most have the characteristic bandicoot shape: a plump, arch-backed body with a long, delicately tapering snout, very large upright ears, relatively long, thin legs, and a thin tail.

Order: Diprotodontia (kangaroos, wallabies, wombats and allies)

Diprotodontia is a large order of about 120 marsupial mammals including the kangaroos, wallabies, possums, koala, wombats, and many others. They are restricted to Australasia.

Subclass Eutheria

Order: Proboscidea (elephants)

The elephants comprise three living species and are the largest living land animals.

Order: Sirenia (manatees and dugongs)

Sirenia is an order of fully aquatic, herbivorous mammals that inhabit rivers, estuaries, coastal marine waters, swamps, and marine wetlands. All four species are endangered.

Order: Scandentia (treeshrews)

The treeshrews are small mammals native to the tropical forests of Southeast Asia. Although called treeshrews, they are not true shrews and are not all arboreal.

Order: Dermoptera (colugos)

The two species of colugos make up the order Dermoptera. They are arboreal gliding mammals found in Southeast Asia.

Order: Primates

The order Primates contains humans and their closest relatives: lemurs, lorisoids, monkeys, and apes.

Order: Rodentia (rodents)

Rodents make up the largest order of mammals, with over 40% of mammalian species. They have two incisors in the upper and lower jaw which grow continually and must be kept short by gnawing. Most rodents are small though the capybara can weigh up to 45 kg.

Order: Lagomorpha (lagomorphs)

The lagomorphs comprise two families, Leporidae (hares and rabbits), and Ochotonidae (pikas). Though they can resemble rodents, and were classified as a superfamily in that order until the early 20th century, they have since been considered a separate order. They differ from rodents in a number of physical characteristics, such as having four incisors in the upper jaw rather than two.

Order Eulipotyphla (shrews, moles, and hedgehogs)

The "shrew-forms" are insectivorous mammals. The shrews and solenodons closely resemble mice while the moles are stout-bodied burrowers. The hedgehogs are easily recognised by their spines while gymnures look more like large rats.

Order: Chiroptera (bats)

The bats' most distinguishing feature is that their forelimbs are developed as wings, making them the only mammals capable of flight. Bat species account for about 20% of all mammals.

Order Pholidota (pangolins)

The order Pholidota comprises the eight species of pangolin. Pangolins are anteaters and have the powerful claws, elongated snout and long tongue seen in the other unrelated anteater species.

Order: Cetacea (whales)

The order Cetacea includes whales, dolphins and porpoises. They are the mammals most fully adapted to aquatic life with a spindle-shaped nearly hairless body, protected by a thick layer of blubber, and forelimbs and tail modified to provide propulsion underwater.

Order: Carnivora (carnivorans)

There are over 260 species of carnivorans, the majority of which feed primarily on meat. They have a characteristic skull shape and dentition.

Order: Perissodactyla (odd-toed ungulates)

The odd-toed ungulates are browsing and grazing mammals. They are usually large to very large, and have relatively simple stomachs and a large middle toe.

Order: Artiodactyla (even-toed ungulates)

The even-toed ungulates are ungulates whose weight is borne about equally by the third and fourth toes, rather than mostly or entirely by the third as in perissodactyls. There are about 220 artiodactyl species, including many that are of great economic importance to humans.

Locally extinct

The following taxa are locally extinct in the country: