In "Starch Fossils and the Domestication and Dispersal of Chili Peppers (Capsicum spp. L.) in the Americas," by Linda Perry inter al. (Science 16 February 2007: 986-988.), Smithsonian Museum scientists explain that they isolated starch microfossils in 7 sites, located in a swath stretching from the Bahamas to Peru.

Some of the samples are 6000 years old; therefore, chile peppers (Capiscum) were mixed with maize even before there was pottery in the Americas. The genus of the chile pepper is believed to have started in Bolivia. This Bolivian plant is not the domesticated form. However, for the domesticated form to appear in the microfossils, cultivation had to have started well before 6000 years ago.

The scientists say that their discoveries show that domesticated capiscum was used as a seasoning rather than as a staple food item, always present together with maize. Once introduced into the diet, chile as a seasoning never left.

USA Today reports in Chiles: Spice of life (and food) through the millennia that chile peppers (from the Capiscum species) have been part of the human diet for 6100 years. So far, the oldest traces of these cultivated peppers come from Ecuador. This is not believed to be the original home of chiles because it is too far from the home of wild chiles.

Also see the Smithsonian article: Smithsonian scientists report ancient chili pepper history and one from Nature.com: Ancient foodies liked it hot.