As a member of the chinense species, the history of the habanero dates back to 6,500 B.C. An intact chinense pod was found in Preceramic levels in Guitarrero Cave in Peru, indicating that it was 8500 years old. The species is thought to have originated in the Amazon basin and was gradually domesticated over many millennia, as locals learned to farm and grow plants. They could then use human selection to breed larger and stronger versions, and by about 1000 B.C., many chinense varieties were domesticated and spread throughout South and Central America, and the Caribbean. After Columbus reached the Caribbean Islands in 1492, he brought back many varieties to the Portuguese, who then spread them to Africa.
The Habanero itself is thought to have originated in Cuba, as it is named after the Cuban city of La Habana, known in the U.S. as Havana, because it used to feature in heavy trading there. It is related to the Scotch bonnet pepper; they have somewhat different pod types but are varieties of the same species and have similar heat levels.
The habanero pepper grows mainly on the Yucatan Peninsula in Mexico, where it is now thought to have originated, though it also grows in other hot climates including in Belize, in Costa Rica, in parts of the United States, and in Panama where it is known as the aji chombo.
Once the Spanish had discovered it, they spread it far and wide around the world, so much so that taxonomists in the 18th century thought it originated in China and therefore named it “Capsicum chinense” or the “Chinese pepper.” If anything, this pepper’s popularity is even more on the rise today.