There are at least 139 mammal species. Of the 16 endemic mammals, 13 are threatened and amongst the 32 threatened species include the critically endangered Malabar large-spotted civet, the endangered lion-tailed macaque and Indian elephants, the vulnerable Indian leopard and gaur These hill ranges serve as important wildlife corridors and forms an important part of Project Elephant and Project Tiger reserves. The largest population of tigers outside the Sundarbuns is in the Western Ghats where there are seven populations with an estimated population size of 336 to 487 individuals occupying forest in three major landscape units spread across Karnataka, Tamil Nadu and Kerala. The Western Ghats eco-region has the largest Indian elephant population in the wild with an estimated 11,000 individuals across eight distinct populations. The Critically Endangered endemic Malabar large-spotted civet is estimated to number fewer than 250 mature individuals, with no sub-population greater than 50 individuals. About 3500 lion-tailed macaques live scattered over several areas in the Western Ghats.

The amphibians of the Western Ghats are diverse and unique, with more than 80% of the 179 amphibian species being endemic to the rainforests of the mountains. The endangered purple frog was discovered in 2003. Several families of are endemic to this region. New frog species were described from the Western Ghats in 2005 and more recently a new species.

There are 288 freshwater fish species are listed for the Western Ghats, including 35 also known from brackish or marine water. There are 118 endemic species, including 13 genera entirely restricted to the Western Ghats 97 freshwater fish species from the Western Ghats were considered threatened in 2011, including 12 critically endangered, 54 endangered and 31 vulnerable. All but one (Tor khudree) of these are endemic to the Western Ghats. An additional 26 species from the region are considered data deficient (their status is unclear at present).

There are at least 508 bird species. Most of Karnataka's five hundred species of birds are from the Western Ghats region. There are at least 16 species of birds endemic to the Western Ghats including the endangered rufous-breasted laughing thrush, the vulnerable Nilgiri wood-pigeon, white-bellied short wing and broad-tailed grass bird, the near threatened grey-breasted laughing thrush, black-and-rufous flycatcher, Nilgiri flycatcher, and Nilgiri pipit, and the least concern Malabar (blue-winged) parakeet, Malabar grey hornbill, white-bellied treepie, grey-headed bulbul, rufous babbler, white-bellied blue-flycatcher and the crimson-backed sunbird.

There are roughly 6,000 insect species. Of 334 Western Ghats butterfly species, 316 species have been reported from the Nilgiri Biosphere Reserve. The Western Ghats is home to 174 species of odonates , including 69 endemics. There are several species of leeches found all along the Western Ghats.

Seasonal rainfall patterns of the Western Ghats necessitate a period of dormancy for its land snails, resulting in their high abundance and diversity including at least 258 species of gastropods from 57 genera and 24 families. A total of 77 species of freshwater molluscs have been recorded from the Western Ghats, This include 28 endemics. 4 species of freshwater molluscs are considered endangered and 3 are vulnerable. An additional 19 species are considered data deficient.