The Kerguelen Islands are part of the Southern Indian Ocean Islands tundra ecoregion, which includes several subantarctic islands. In this cold climate, plant life is mostly limited to grasses, mosses, and lichens, though the islands are also known for the native and edible Kerguelen cabbage. The islands are located at the Antarctic Convergence, where cold water from Antarctica mixes with warmer water from the Indian Ocean. Because of this, marine mammals, especially seals, as well as seabirds and penguins, are found in large numbers.

Fauna

Seals and fur seals:
• Southern elephant seal (Mirounga leonina)
• Antarctic fur seal (Arctophoca gazella)
• Leopard seal (Hydrurga leptonyx) occasional

• Commerson's dolphin (Cephalorhynchus commersonii)
• Type D or Sub-Antarctic orca (Orcinus orca)
• Humpback whale (Megaptera novaeangliae)
• Southern right whale (Eubalaena australis), etc.

Introduced land mammals:
• Bizet sheep. Approximately 3,500 partially wild sheep once lived on Ile Longue; they were mainly kept to provide meat for scientists living on the islands. The Bizet sheep are an endangered breed in France, where they originally came from. On Kerguelen, the baby sheep have higher death rates because they do not adapt well to the Southern Hemisphere. The ewes often gave birth in winter, when food is scarce, or in midsummer, after the best spring period. By 2014, there were 150 male Bizet sheep with no females.

• Mouflons (mountain sheep). About 100 individuals lived on the islands. They were brought from Corsica in 1959 and were kept only on Haute Island in the Golfe du Morbihan. The population was removed by 2012 as part of efforts to eliminate introduced species.

• Reindeer. Reindeer were brought to Ile des Rennes (also called Ile Australia) by Norwegians. They are good swimmers and quickly swam to the main island, La Grande Terre. Today, about 4,000 reindeer live on the islands. They survive by eating lichens and mosses, but their presence harms the islands' plants. These are the only reindeer in the Southern Hemisphere, apart from a similar population on South Georgia, which was almost removed by 2013, with the last two killed in 2017.

• Rabbits. These small animals were brought from South Africa in 1874 and reintroduced later. They were added to provide food for sailors who might be stranded. Rabbits have damaged the islands' plants and caused serious erosion, especially on the eastern half of the islands, where their numbers reached 40+ per acre in some areas. The western and northwestern parts of the islands are less affected because the climate is harsher. Rabbits were also introduced to Ile Verte but were removed by 1992.

• Rats and mice. These were brought to the islands by ships hunting seals and whales.

• Cats. Feral cats live on the islands. They are descendants of cats kept by sailors to control rats. Cats mainly eat mice, rabbits, and albatross chicks. A second group of cats was introduced in 1956.

• Dogs. These were brought to the islands by ships hunting seals and whales. Feral dogs were reported between 1852 and 1951 but have not been seen since.

• Equines. Mules were brought to Port-aux-Français in 1948 and lived there for five years. Shetland ponies were also reported to live there in the 1950s.

Birds:
• King penguin (Aptenodytes patagonicus)
• Gentoo penguin (Pygoscelis papua)
• Southern rockhopper penguin (Eudyptes chrysocome)
• Macaroni penguin (Eudyptes chrysolophus)

• Albatross
• Black-faced sheathbill
• Cormorants
• Kerguelen petrel
• Kerguelen shag
• Seagulls
• Prions
• Skuas
• Kerguelen tern

The Kerguelen Islands are protected by France's agreement to the International Agreement on the Conservation of Albatrosses and Petrels, which was created under the Convention on Migratory Species.

• Eaton's pintail (Anas eatoni)
• Mallard (Anas platyrhynchos) introduced

In the 1950s and 1960s, a French geologist named Edgar Albert de la Rue introduced several species of salmonids. Of the seven species introduced, only brook trout (Salvelinus fontinalis) and brown trout (Salmo trutta) survived and formed wild populations. Brook trout live in headwater streams, while brown trout live in both streams and in the sea.

Insects:
• Calycopteryx mosleyi, a fly that lives near the Kerguelen cabbage
• Meropathus chuni, a very small aquatic beetle
• Anatalanta
• Palirhoeus eatoni

Introduced species:
• Oopterus soledadinus, a large ground beetle
• Merizodus

Flora

The coastal areas, up to about 50 meters above sea level, are usually covered with low-growing grasses and plants, and are called tundra. At higher elevations, rocky ground is common, and plant life is rare, with only scattered mosses, lichens, and small patches of vegetation.

There are no trees or shrubs on the islands. This was not always true. Fossilized tree trunks from the Araucariaceae family have been found in some sediments, showing that Kerguelen once had a warmer climate.

Originally, the main low-altitude vegetation was a thick, continuous layer of azorellae (Azorella selago), which supported other plants like the Kerguelen cabbage (Pringlea antiscorbutica). Azorellae grew in rounded, pillow-like shapes, with each year’s growth forming a tight layer on top of the previous one. The species Lyallia kerguelensis (Hectorellaceae), the only plant found only on the archipelago, has a similar growth pattern. These azorellae pillows could be more than 1 meter thick, and neighboring plants could join to form a continuous sheet. Walking on this vegetation was difficult and harmful to the environment. However, it provided a good nesting ground for some marine birds that dug burrows in the plant layers.

The introduction of rabbits destroyed this habitat, replacing it with a meadow made up of a single type of plant, Acaena adscendens (Rosaceae), which resembles a small salad burnet. Today, azorellae carpets are only found on islands and islets not affected by rabbits. The Kerguelen cabbage faced a similar decline. Other mammals also affected the vegetation, such as mice eating the seeds of the Kerguelen cabbage and reindeer consuming lichens.

In flat, low areas near streams, the ground is often wet. A type of boggy vegetation made mostly of mosses can grow there. While this vegetation may look uniform on the surface, it can cover quicksand, where hikers might sink up to their waist.

Unlike the limited land vegetation, the marine plants are abundant, especially the giant brown algae. Kelp (Macrocystis pyrifera) forms underwater forests, and cochayuyo (Durvillaea antarctica) covers most rocky coasts.

Kelp is one of the largest types of marine algae, growing up to 50 meters long. It attaches to the seafloor with branched structures and grows upward in columns of interwoven strands. At the top, floating structures help the kelp spread widely. These underwater forests can cover large areas, making navigation difficult because their thin strands may tangle with ship propellers. The kelp forests are home to many colorful invertebrates and red algae, but few vertebrates. Storms often tear large amounts of kelp from the forests, which wash ashore and rot on beaches, forming thick layers. These algae deposits are a key part of the local ecosystem.