Fiordland National Park contains a great biodiversity. Common birds include tomtits, brown creepers, grey warblers, fantails, tui, bellbirds, kereru, kea and kaka.
Many species within Fiordland are threatened due to the lack of habitat or introduced predators. These species are: takahe (Porphyrio hochstetteri), yellow-crowned parakeet (Cyanoramphus auriceps), yellowhead (Mohoua ochrocephala), the long-tailed bat (Chalinolobus tuberculatus), the brown teal (Anas chlorotis), the blue duck (Hymenolaimus malacorhynchos), the southern crested grebe (Podiceps cristatas australis), pied shag (Phalacrocorax varius varius), New Zealand falcon (Falco novaeseelandiae), the South Island saddleback (Philesturnus carunculatus) and the southern brown kiwi (Apteryx australis australis).
Since most of the fiords have a freshwater layer caused by melting glaciers, Fiordland is home to significant populations of the black coral (Antipatharia), brachiopods, sponges and starfish. That might be one reason why its coastline attracts many marine species such as the bottlenose dolphins (Tursiops truncatus), New Zealand fur seals (Arctocephalus forsteri), Fiordland crested penguins (Eudyptes pachyrhynchus) and little blue penguins (Eudyptula minor). Several whale species are regular visitors.
Common insects include the sandfly (Austrosimulium unulatum), alpine cicadas (Maoricicada cicada), tussock butterflies (Lycaena salustius), weevils, winter mosquitoes and many more.
Introduced animals are rats, mice, stoats, hares, deer and possums.