Mutualists is when two organisms of different species have a beneficial relationship between each other. Example of mutualists that can be found in Kapas's reef is the sea anemone and the clownfish. The sea anemone provides habitat and shelter for the clown fish, in return gain essential nutrients from the clown fish waste products. Sometimes, the clown fish will also scare away predators that wants to predate on sea anemone.

Animals such as damselfish and parrotfish that eat plants including algae, phytoplankton, seaweed and seagrass are also considered keystone species. These herbivores helps in controlling the biology and physical aspect of the ecosystem. For example, parrotfish's waste products contributes to the fine sand texture in Pulau Kapas.

Predators control the balance of prey population in the reef ecosystem. This can prevent from herbivorous fish to overgraze the corals. For example, the predator in Kapas's reef are the black-tip reef shark. Sharks also eat sick fish and simultaneously removing any potential disease to spread in the ecosystem.

Ecosystem engineers are organisms that influence the physical shape of the reef structure. They serves as a important fundamental building blocks of the entire reef ecosystem. Example of engineers organisms that can be found in Kapas's reef are diverse species of corals and giant clams.