Origins
The Amazon basin was the center of origin for the chinense species, but the story of the spread of the wild varieties and their eventual domestication is still not clear. However, the oldest known chinense specimen ever found was a single intact pod (probably a wild form) that was discovered in Preceramic levels (6,500 B.C.) in Guitarrero Cave in coastal Peru.
Since both wild and domesticated forms of the Brazilian chinense exist today, it follows that the species was domesticated much in the same manner as the annuum species was in Mexico. First, it was a tolerated weed with erect fruits. Then, as early farmers planted the seeds and tended the plants, there was a gradual evolution by human selection to larger, more pendant pods.
The domestication of the chinense species occurred around 2000 B.C., and, according to ethnobotanist Barbara Pickersgill, "it was probably connected with the development of agriculture in tropical forests. It seems reasonable to assume that C. chinense was domesticated east of the Andes by these tropical forest agriculturists, who were probably responsible for the domestication of manioc." She added, wryly: "As a condiment, the chile pepper probably formed a welcome addition to any diet consisting largely of manioc starch." By about 1000 B.C., domesticated chinense varieties had spread to the Pacific coast of Peru.
The cultivation of the chinense species produced many pod types and varieties. Bernabe Cobo, a naturalist who traveled throughout South America during the early seventeenth century, probably was the first European to study the chinense species. He estimated that there were at least forty different pod types of the chiles, "some as large as limes or large plums; others, as small as pine nuts or even grains of wheat, and between the two extremes are many different sizes. No less variety is found in color...and the same difference is found in form and shape."
Chinense was and still is the most important cultivated pepper species east of the Andes in South America. Barbara Pickersgill notes that the fruit characteristics of the species are more variable around the mouth of the Amazon than further west because of human selection of the pods.
The dispersion of domesticated chinense types into the Caribbean and Central America occurred in two different directions. Some chinense varieties spread into the Isthmus from Colombia and eventually became common in Panama and Costa Rica. But apparently their spread north was halted before they reached the Yucatán Peninsula. Meanwhile, during their great migrations, the ancestors of the Arawaks and Caribs transferred the chinense from the Amazon Basin through Venezuela and into the Caribbean, where pod types developed on nearly every island. Pickersgill believes that the habanero was "a historic introduction from the West Indies" into Yucatán, completing the chinense's island-hopping encirclement of the Caribbean Sea.
http://www.fiery-foods.com/pepper-profiles/153-chinense-species/97-pepper-profile-habanero