Several decades before the events of Annihilation, the region that now comprises Area X underwent a transformation, the nature of which has never been fully determined. The region became separated from the outside world by an invisible border, and all communication with the inhabitants behind the border was lost. Any objects, whether vehicles, animals or people, that passed through the border from the outside world inexplicably vanished and could not be recovered. Following the appearance of the border, a government agency known as the Southern Reach was established to study Area X and its anomalous properties.
We learn in the book there is a map of Area X although it appears that some places are not documented such as the tower/tunnel that the 12th expedition explored. Some of the places in Area X that are visited in Annihilation included a lighthouse, the marshes, and a base-camp. There is also a border that separates Area X from the rest of the world. When the psychologist is dying, she confesses that the border is moving north. In other words, Area X is expanding.
Area X was inspired by St. Mark's Wildlife Refuge in North Florida. It is "more or less, a transformed version of the fourteen-mile hike [author Jeff VanderMeer] did for almost twenty years at the St. Marks Wildlife Refuge in North Florida." Many of the animals and vegetation that VanderMeer has seen on this hike over the past 17 years appear in the novel. In March 2014, as part of a piece on VanderMeer and Annihilation, he visited the St. Marks Lighthouse that inspired one of the settings in Annihilation.