Ironically, the isolation that allowed Madagascar and its neighboring islands to evolve a diverse and unique fauna and flora also contributed to its environmental degradation. Because humans did not arrive on the islands until 1,500-2,000 years ago, native animals were naïve and easily slaughtered by the colonists. The islands' location off the coast of Africa made them important stopping off points on trade routes and havens for pirates. On the Mascarenes, there is evidence to suggest that the extinction spasm of much of the native megafauna was directly related to hunting.
The Malagasy people came to Madagascar from Africa and Asia and imported agricultural methods, like rice cultivation, slash-and-burn agriculture, and cattle grazing, which are inappropriate for infertile, lateritic soils and devastating to the fragile ecosystems of the island. The central plateau of Madagascar is almost completely deforested - a lifeless moonscape of infertile, baked red earth. It is estimated that only about 17 percent of the original vegetation of Madagascar remains, with most remaining forests found along the eastern, western, and southern coasts. In the Comoros, which had the fourth highest deforestation rate in the world in the early 1990s (5.8 percent per annum), natural forests have been largely replaced with plantations, and the islands have lost at least 80 percent of their native vegetation. On the Seychelles, lowland forests have been cleared for timber production and agriculture, particularly for coconut plantations and cinnamon exploitation.
Mauritius has one of the highest human population densities in the world at 538 persons per square kilometer. In comparison, the nearly 18 million people who live in Madagascar today do not represent a very large number considering the land area of the island. However, the population is growing at more than 3 percent per year and is expected to double by the year 2025. In an area that is already one of the most economically disadvantaged in the world, this growth rate is putting tremendous pressure on the natural environment. In addition to agriculture, hunting and timber extraction, industrial and small-scale mining are growing threats.
On the other Indian Ocean Islands, these same threats have been exacerbated by the introduction of invasive alien species, brought as food sources, pets, or for pest control. Rats, cats and mongooses have devastated populations of birds and small reptiles, while grazing rabbits, goats, pigs, and deer have denuded many landscapes. In addition, exotic plant species such as water hyacinth (Eichhornia crassipes) threaten the biodiversity of freshwater ecosystems in the hotspot.