Hong Kong's climate and physical environment provide a wide range of habitats and support a rich and varied fauna. These include about 450 species of birds, 50 species of mammals, 80 species of reptiles, 23 species of amphibians, 230 species of butterflies and 110 species of dragonflies.

The Mai Po Marshes form one of the most important wildlife conservation sites in Hong Kong. Together with the Inner Deep Bay area, the Mai Po Marshes area has been listed as a 'Wetland of International Importance' under the Ramsar Convention. About 1 500 hectares of mudflats, fish ponds, marshes, reedbeds and dwarf mangroves provide a rich habitat for migratory and resident birds, particularly ducks and waders. Some 300 species of birds have been observed in this area, many of which are considered globally threatened and endangered, such as the black-faced spoonbill, Oriental stork, Nordmann's greenshank and Saunders' gull. The AFCD implements a wetland conservation and management plan to conserve the ecological value of the area.

The traditional fung shui woods near old villages and temples and the secondary forests provide important habitats for many woodland birds. Sightings in wooded areas include warblers, flycatchers, robins, bulbuls and tits.

Areas around the Kowloon reservoirs are inhabited by monkeys descended from individuals that had been released or had escaped from captivity. There are breeding groups of long-tailed macaques and rhesus macaques, and their hybrids. Feeding of monkeys has been prohibited since July 1999 to prevent unnatural growth of the monkey population. Other mammals like barking deer, leopard cats, Chinese porcupines, Chinese ferret badgers, masked palm civets, small Indian civets, wild boars and bats are quite common in the countryside. Sightings of less common species such as Eurasian otters, Javan mongooses and Chinese pangolins are occasionally reported.

Hong Kong has over 100 species of amphibians and reptiles. There are 23 species of amphibians and three of them — the Hong Kong cascade frog, the Hong Kong newt and Romer's tree frog — are protected by the Wild Animals Protection Ordinance due to their endemic status or very restricted distribution in Hong Kong. Most of the 50 species of snakes are harmless, and reports of people being bitten by highly venomous snakes are very rare in Hong Kong. Among the nine native species of chelonians, the green turtle is of particular interest as it is the only known species of sea turtle breeding locally. In 2003, a satellite-tracking study by AFCD on two green turtles nesting in Hong Kong showed that these two turtles migrated to feeding grounds in the coastal waters off Hainan Island.