The patterns of biological diversity in Indo-Burma have resulted from the interaction of topography, Pleistocene climate changes, soil characteristics, and the region's seasonal rainfall. Mountain ranges are minor hotspots of endemism within the larger hotspot, and temperate fauna like pandas, tigers, and salamanders retain a presence in these forests. The most species rich ecosystems in Indo-Burma are the lowland wet evergreen forests. The region's montane forests are less diverse than their lowland counterparts but support more endemic species.

Plants
Knowledge of plant species within the Indo-Burma hotspot is uneven and is hampered by socio-political divisions and strife. A conservative estimate of total plant diversity in the hotspot reveals about 13,500 species, of which about 7,000 (51.9 percent) are endemic. A remarkable 20 Centers of Plant Diversity and Endemism were identified in Indo-Burma in a recent World Conservation Union (IUCN)/World Wildlife Fund (WWF) analysis. Among the most notable plants are a wide array of orchid and ginger species and many fine tropical hardwood trees, including dipterocarp species and teak (Tectona grandis).

Vertebrates
Conservative estimates of terrestrial vertebrate diversity count 2,185 total species, with 528 (24.2 percent) endemic to Indo-Burma.

Birds
The greater adjutant stork is one of the most critically endangered species of birds. The Brahmaputra Valley remains the last stronghold of the bird. There are 1,170 bird species found in Indo-Burma; 140 of these are endemic including, remarkably, some migratory species whose entire migration route is confined within the hotspot. No less than 49 bird species in Indo-Burma are threatened. The hotspot is home to 10 different hornbill species from the family Bucerotidae. These species are excellent indicators of forest health because they depend on mature trees in intact forests to establish their nests. At least 1 hornbill species is threatened in the region: the rufous-necked hornbill (Aceros nipalensis) has been extirpated from much of its range by habitat destruction. Birdlife International has identified 8 Endemic Bird Areas (EBAs) in the hotspot. Critically endangered bird species in these regions are the white-eared night heron (Gorsachius magnificus) of Hainan Island, the beautiful imperial pheasant (Lophura imperialis), and Edward's pheasant (Lophura edwardsi) of the Annamese Lowlands, the orange-necked partridge (Arborophila davidi) of the South Vietnamese Lowlands, and the gray-crowned crocias (Crocias langbianis) of Vietnam's Da Lat Plateau.

Mammals
There are 329 mammal species in the hotspot, including 122 bats and 81 rodents; 73 species and 8 genera are endemic. An indication of the relative lack of knowledge about mammal diversity in this region is the number of species that have been discovered in recent years. The Truong Son muntjac (Muntiacus truongsonensis), a new species of deer, was described in 1998. The saola (Pseudoryx nghetinhensis) and the giant muntjac deer (Megamuntiacus vuquangensis) represent completely new and endemic genera. In addition, the Vietnamese warty hog (Sus bucculentus) was recently rediscovered. Other mammal species that represent important conservation priorities include the endemic Eld's deer (Cervus eldi), which is confined to a few isolated populations of only several hundred individuals. Additionally, each population is recognized as a distinct subspecies. The hotspot is important habitat for more widespread endangered species, such as the Asian elephant (Elephas maximus) and the tiger (Panthera tigris). Indo-Burma is extremely rich in endemic primate species. Several are restricted to isolated areas of Vietnam and Laos, including six subspecies of Vietnamese karst monkeys (Presbytis francoisi), the strikingly beautiful northern Douc langur (Pygathrix nemaeus nemaeus), and the remaining Tonkin snub-nosed monkeys (Rhinopithecus avunculus) whose population numbers only in the hundreds. The region is also home to five endemic species of gibbons, important indicators of forest health.

Reptiles
At least 484 retile species are found in the hotspot; 201 species and 13 genera are endemic. Endemism is especially high among the skinks and snakes of the Colubidae family. Additionally, Indo-Burma supports the highest diversity of freshwater turtles in the world: 43 species in 29 genera and four families representing 17 percent of the world's turtle species and more than 25 percent of world turtle genera. The Siamese striped giant soft-shelled turtle (Chitra chitra) can reach sizes over 120 centimeters long and is the largest freshwater turtle species in the world. Other notable reptiles are the Siamese crocodile (Crocodylus siamensis), which may only remain in captive breeding populations in the region, and the butterfly lizards of the genus Leiolepis.

Amphibians
There are 202 amphibian species in the Indo-Burma hotspot, 114 are endemic. However, endemism does not extend to the genus level; only 2 genera of more than 40 are restricted to the region. The Tam-Dao salamander (Paramesotriton deloustali), a large brown salamander with an orange belly, is the flagship amphibian for the region. Other interesting amphibians include the horned toad-frog (Megophrys carinensis) and the Taylorana hascheana, a frog with a distinctive crow-like mating call.