Sea otters protect kelp forests from damage by sea urchins. When the sea otters of the North American west coast were hunted commercially for their fur, their numbers fell to such low levels – fewer than 1000 in the north Pacific ocean – that they were unable to control the sea urchin population. The urchins, in turn, grazed the holdfasts of kelp so heavily that the kelp forests largely disappeared, along with all the species that depended on them. Reintroducing the sea otters has enabled the kelp ecosystem to be restored. For example, in Southeast Alaska some 400 sea otters were released, and they have bred to form a population approaching 25,000.

Keystone predators may increase the biodiversity of communities by preventing a single species from becoming dominant. They can have a profound influence on the balance of organisms in a particular ecosystem. Introduction or removal of a keystone predator, or changes in its population density, can have drastic cascading effects on the equilibrium of many other populations in the ecosystem. For example, grazers of a grassland may prevent a single dominant species from taking over.

The elimination of the gray wolf from the Greater Yellowstone Ecosystem had profound impacts on the trophic pyramid. Without predation, herbivores began to over-graze many woody browse species, affecting the area's plant populations. In addition, wolves often kept animals from grazing in riparian areas, which protected beavers from having their food sources encroached upon. The removal of wolves had a direct effect on beaver populations, as their habitat became grazing territory. Increased browsing on willows and conifers along Blacktail Creek due to a lack of predation caused channel incision because the beavers helped slow the water down, allowing soil to stay in place. Furthermore, predation keeps hydrological features such as creeks and streams in normal working order. When wolves were reintroduced, the beaver population and the whole riparian ecosystem recovered dramatically within a few years.

As described by Paine in 1966, some sea stars (e.g., Pisaster ochraceus) may prey on sea urchins, mussels, and other shellfish that have no other natural predators. If the sea star is removed from the ecosystem, the mussel population explodes uncontrollably, driving out most other species.

These creatures need not be apex predators. Sea stars are prey for sharks, rays, and sea anemones. Sea otters are prey for orca.

The jaguar, whose numbers in Central and South America have been classified as near threatened, acts as a keystone predator by its widely varied diet, helping to balance the mammalian jungle ecosystem with its consumption of 87 different species of prey. The lion is another keystone species.

Keystone mutualists are organisms that participate in mutually beneficial interaction, the loss of which would have a profound impact upon the ecosystem as a whole. For example, in the Avon Wheatbelt region of Western Australia, there is a period of each year when Banksia prionotes (acorn banksia) is the sole source of nectar for honeyeaters, which play an important role in pollination of numerous plant species. Therefore, the loss of this one species of tree would probably cause the honeyeater population to collapse, with profound implications for the entire ecosystem. Another example is frugivores, such as the cassowary, which spreads the seeds of many different trees. Some seeds will not grow unless they have been through a cassowary.

A term used alongside keystone is ecosystem engineer. In North America, the prairie dog is an ecosystem engineer. Prairie dog burrows provide the nesting areas for mountain plovers and burrowing owls. Prairie dog tunnel systems also help channel rainwater into the water table to prevent runoff and erosion, and can also serve to change the composition of the soil in a region by increasing aeration and reversing soil compaction that can be a result of cattle grazing. Prairie dogs also trim the vegetation around their colonies, perhaps to remove any cover for predators. Grazing species such as plains bison, which is another keystone species, the pronghorn, and the mule deer have shown a proclivity for grazing on the same land used by prairie dogs.

The beaver is a well known ecosystem engineer and keystone species. It transforms its territory from a stream to a pond or swamp. Beavers affect the environment first altering the edges of riparian areas by cutting down older trees to use for their dams. This allows younger trees to take their place. Beaver dams alter the riparian area they are established in. Depending on topography, soils, and many factors, these dams change the riparian edges of streams and rivers into wetlands, meadows, or riverine forests. These dams have been shown to be beneficial to a myriad of species including amphibians, salmon, and song birds.

In the African savanna, the larger herbivores, especially the elephants, shape their environment. The elephants destroy trees, making room for the grass species and creating habitat for various small animal species. Without these animals, much of the savanna would turn into woodland. In the Amazon river basin, peccaries produce and maintain wallows that are utilized by a wide variety of species. Australian studies have found that parrotfish on the Great Barrier Reef are the only reef fish that consistently scrape and clean the coral on the reef. Without these animals, the Great Barrier Reef would be under severe strain.

In the Serengeti, the presence of sufficient gnus in these grasslands reduces wildfire likelihood, which in turn promotes tree growth. The documentary The Serengeti Rules documents this in detail.

The community ecologist Bruce Menge states that the keystone concept has been stretched far beyond Paine's original concept. That stretching can be quantified: the researcher Ishana Shukla has listed 230 species identified as keystones in some 157 studies in the 50 years since Paine's paper. Menge's own work has shown that the purple Pisaster sea star that Paine had studied was a powerful keystone species in places exposed to strong wave action, but was far less important in sheltered places. Paine had indeed stated that in Alaska, without the relevant mussel species as prey, the predatory Pisaster was "just another sea star". In other words, the extent to which a species could be described as a keystone depended on the ecological context.

Although the concept of the keystone species has a value in describing particularly strong inter-species interactions, and for allowing easier communication between ecologists and conservation policy-makers, it has been criticized by L. S. Mills and colleagues for oversimplifying complex ecological systems. The term has been applied widely in different ecosystems and to predators, prey, and plants (primary producers), inevitably with differing ecological meanings. For instance, removing a predator may allow other animals to increase to the point where they wipe out other species; removing a prey species may cause predator populations to crash, or may allow predators to drive other prey species to extinction; and removing a plant species may result in the loss of animals that depend on it, like pollinators and seed dispersers. Beavers too have been called keystone, not for eating other species but for modifying the environment in ways that affected other species. The term has thus been given quite different meanings in different cases. In Mills's view, Paine's work showed that a few species could sometimes have extremely strong interactions within a particular ecosystem, but that does not automatically imply that other ecosystems have a similar structure.

• Cultural keystone species
• Ecosystem service
• Foundation species
• Indigenous
• Introduced species
• Sentinel species

• Caro, Tim (2010). Conservation by proxy: indicator, umbrella, keystone, flagship, and other surrogate species. Washington, DC: Island Press. ISBN 9781597261920.