Bhitarkanika presents a variety of habitats, microhabitat and climatic conditions. Therefore, the faunal component and faunal diversity is also extremely high in comparison to other mangrove forest areas of Orissa. The habitat diversity includes agricultural fields, rivers, fresh water ponds, rich mangrove vegetation, tidal rivers, creek and creek lets, estuaries, mud flats, fresh water and brackish water wetlands, river line islands, off shore islands, muddy and sandy coast line etc. which provide home for a varied and large number of animal species. Mangroves serve as roosting, nesting, feeding, breeding and nursery ground of tidal rivers in tidal forests and in the estuarine food web. Mangrove plants are the source of rich food for the organisms of the mangrove ecosystem. The animals that are associated with the mangroves cover a wide range of vertebrate and other invertebrates including protozoans and zoo planktons. The vertebrate fauna includes a wide variety of fishes, amphibians, birds, reptiles and mammals including aquatic mammals. Because food and shelter is not a limiting factor in Bhitarkanika. The number of animals of a species are also very rich. Bhitarkanika Sanctuary is home for the largest number of salt water Crocodiles in the country. "Bagagahana" the heronry provides nesting and living space to about 80,000 resident and local migratory birds. Also the numerous wetlands scattered throughout the Sanctuary serve as feeding and wintering grounds for more than 50,000 migratory birds during winter and early summer months. The Sanctuary is the World's largest nesting ground of the endangered Olive Ridley sea turtle(Lepidochelys Olivacea).

Mangrove ecosystem supports a range of interconnected food chains which directly sustain the fisheries to exist. Algae and detritus sustain shrimps and prawns which provide a food source for species such as Bhekti (Lates Spp.). Cat fishes, etc. Fish and prawns spend most of their adult life at sea and return to the mangrove areas where they spend their early life. Some of the commercially important fishes are illisha (Hilsa illisha). Khainga (Mullet Spp.). Bhekti (Lates calcifer). Kantia (Mustus qulio). Kokill or Anchovy (Coilia dussumier) etc. Some fish species that are of interest as aquarium fishes include Rice fish (Oryzias melastigma), Panchx (Aplocheilus ponchax). Puffer fish (Chelonodon fluviafilis). Terapon jurbua. Acer fish (Toxotes Jaculator), Climbing Perch (Anabas testudineus). Dwart gourami (Colisa lalia). Species Eleotrid (Sleeper). Glass fish (Chanda Spp.). Pipe fishes, Mud skippers (Periophthalmus and Bolephthalmus Spp.) etc. The mud skippers are able to survive short periods of aerial exposure, skip around on the water and mud and build chimney like burrows in muddy banks of river and creeks through out the Sanctuary.
In the whole of South-East Asia as well as in the Northern Indian Ocean countries Bhitarkanika is famous for its reptilian fauna. It is an unique reptilian refuge. The reptilian fauna is largely dominated by Indo-Chinese elements. The longest estuarine crocodile of the World measuring more than seven meters long are located here.

Mud Dwellers :
The animals found in the mangrove community. according to their habitats can be categorized as Mud dwellers. the aquatic inhabitants restricted to the water ways, Forest dwellers found in the forests and Canopy dwellers found in the tree canopy.
The mangrove mud is a very special habitat which may further provide a variety of microhabitats. The mud-dwelling animals or the mud dwellers show fascinating unusual features of structure, function and behaviour of which are characteristics of the amphibious fish (Periopththalmus and Bolephthalmus spp.) and a variety of crabs and molluscs. These mud dwellers are abundantly found along all river banks and mud flats of the Bhitarkanika mangrove area. About eight species of crabs are found.

King crabs or the Horse-shoe crabs find their way to Bhitarkanika mud flats for their mating and laying of eggs,where their pre-historic trilobite larvae thrived in the pristine and primitive Bhitarkanika mangrove atmosphere. Out of the four species of horse shoe crabs of the World, two species are found in India viz; Tachypleus gigas and Carcinoscorpious rotundicauda. Both these species are found in Bhitarkanika along Gahirmatha coast (Brahmani-Baitarani delta) and in the adjoining Mahanadi delta. King crabs are slaughtered widely for the extraction of the highly priced chemical "lectine" as a result of which they have become threatened globally. Fortunately enough, Bhitarkanika provides all conducive environmental conditions to nourish both species of Indian horse shoe crabs.

The other interesting crab species is the Feeder crabs (Uca spp.) Hermit crabs and Horseshoe crabs. Other mud dwellers include varieties of snails and bivalves. Among the crustaceans. the tiger prawn Peneaus monodon is the main economic attraction of the tidal creeks rivers, estuaries and off shore coastal waters. Though the prawns breed in sea. the post larval stages of the species are nourished in the high nutrient rich nursery of the mangrove environment till they reach the adult stage. Other important prawns include Peneaus indicus and Metapeneaus affinis etc.