Although people arrived in New Zealand relatively late—about 700-800 years ago—human effects on the land and natural ecosystems have been extensive. The first great impact was from hunting, fishing and gathering by Maoris, which caused the extinction of native bird species such as the giant moas and eagles.

However, an even greater threat to the native biodiversity of the hotspot was the introduction of invasive alien species. When Europeans arrived on the islands in the early nineteenth century, they brought with them 34 exotic mammal species (including brush-tailed possums, rabbits, cats, goats, stoat, ferrets and many European bird species) and hundreds of exotic plant species, some of which have become invasive. In conjunction with the impact of hunting (and also extensive habitat destruction), the last two hundred years have witnessed the extinction of 16 land birds, one endemic bat, one fish, at least a dozen invertebrates and 10 plants. Several other species survive only in tiny populations on offshore islands.

Today, invasive alien species remain an important threat to New Zealand's biodiversity, but large-scale habitat destruction, through deforestation, wetland drainage and ecosystem degradation, represents as serious an issue.