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The particularity of Masoala is its terrestrial ecosystem, which is characterised by rainforests ranging from 0m to 1,300m above sea level. Masoala is one of the rare regions of Madagascar where the edge of the forest literally meets the sea. A fragile forest corridor joins the forest of the Masoala peninsula with the [[Anjanaharibe Sud Special Reserve|Anjanaharibe-Sud Special Reserve]] and the [[Makira Plateau]]. The existence of the corridor is essential to prevent Masoala from becoming an isolated ecosystem in terms of wildlife.

The marine and coastal ecosystem is characterised by several forest and rock patches, sandy bays, coral reefs, seagrass beds and narrow strips of mangrove forest.