The flora and fauna of Ladakh was first studied by Ferdinand Stoliczka, an Austrian/Czech palaeontologist, who carried out a massive expedition in the region in the 1870s. The fauna of Ladakh have much in common with that of Central Asia generally, and especially those of the Tibetan Plateau. An exception to this are the birds, many of which migrate from the warmer parts of India to spend the summer in Ladakh. For such an arid area, Ladakh has a great diversity of birds — a total of 225 species have been recorded. Many of these birds reside or breed at high-altitude wetlands such as Tso Moriri.

Many species of finches, robins, redstarts (like the Black Redstart) and the Hoopoe are common in summer. The Brown-headed Gull is seen in summer on the river Indus, and on some lakes of the Changthang. Resident water-birds include the Brahminy duck also known as the Ruddy Sheldrake, and the Bar-headed Goose (Ladakhi: ngangpa). The Black-necked Crane (trhung-trhung) is a rare species found scattered in the Tibetan plateau, and is also found nesting in summer in parts of Ladakh. Other birds include the Raven, Red-billed Chough (chungka), Tibetan Snowcock and Chukar (a partridge, srakpa) . The Lammergeier and the Golden Eagle are common raptors here.

A list of the bird species recorded is as follows:

The ibex (Ladakhi: skin) is found in high craggy terrain of Europe, North Africa and Asia, and numbers several thousand in Ladakh: trekkers often spot them. The Bharal or "blue sheep" (napo) is even more common, ranging in the Himalayas from Ladakh east as far as Sikkim. The Tibetan Urial sheep (shapo) is a rare goat found at lower elevations, mostly in river valleys, and therefore is often directly in competition with domesticated animals. They are now rare, numbering about one thousand. The Tibetan Argali sheep (nyan) is a relative of the Marco Polo sheep of the Pamirs. Impressive animals with huge horizontal curving horns, they are extremely rare in Ladakh, numbering only a couple hundred, but they do have a wide range throughout mountainous areas of the Chinese Provinces of Xinjiang, Qinghai, and Gansu. The habitat of the extremely rare Tibetan Gazelle (gowa) is near the Tibetan border in southeastern Ladakh. The musk deer (lhawa) has not been seen in Ladakh for decades if not generations.

The Tibetan Antelope, (Ladakhi: tsos, Indian English chiru) is also endangered. Early in the 20th century the chiru was seen in herds of thousands, surviving on remarkably sparse vegetation, but they are vanishingly rare now. It has been hunted for its fine under-wool (Urdu: shahtoosh, Ladakhi: tsoskul), which must be pulled out by hand, a process done after the animal is killed. This shahtoosh is valued in South Asia for its light weight and warmth, but more than anything else, as a status symbol. Owning or trading in shahtoosh is now illegal in most countries.

The Tibetan Wild Ass (Ladakhi: kyang) is one animal that visitors can expect to see from the comfort of a vehicle, if they take a jeep tour on the Changthang. Favouring the rolling grasslands of this area, their natural curiosity makes them fairly easy to spot, despite the relatively low numbers, about 1500 individuals.

The Snow Leopard (Ladakhi: shan) once ranged throughout the Himalaya, Tibet, and as far as the Sayan mountains on the Mongolian-Russian border; and in elevation from 1800m to 5400m. They are extremely shy and hard to spot, and as such not well known. It is believed there are about 200 in Ladakh. While tourists are unlikely to see leopards themselves, during winter the footprints and other marks are not uncommon. Other cats in Ladakh are even rarer than the snow leopard: the Lynx (ee), numbering only a few individuals, and the Pallas's cat, which looks somewhat like a house cat. The Tibetan Wolf (shangku) is the greatest threat to the livestock of the Ladakhis and as such is the most persecuted. There are only about 300 wolves left in Ladakh. There are also a very few brown bears (drenmo / tret) in the Suru valley and the area around Dras. The red fox is common, and Tibetan Sand Fox has recently been discovered in this region (both: watse).

Among smaller animals, marmots (Ladakhi: pheya) are common; you can even sometimes see them from the road, although they do not look very different from the marmots common to other mountainous areas of the world. There are also plenty of hares (ribong), and several types of voles and pika (both: rdzabra / zabra).

A full list of mammals based on Pfister is as follows: