The aim of this work was to determine in Capsicum chinense the 1) concentration of heavy metals (Al, As, Cd, Pb), majority (Ca, K, Mg, Na) and essential (Cu, Fe, Mn, Se, Zn) mineral elements, 2) effects of ripening stage, harvest number and type of soil on the mineral content and 3) authenticity markers. Peppers grown in black and red soils of this Mayan region, were harvested in two ripening stages (ripe and ripening peppers [orange and green peppers, respectivily]) and in four post-transplant dates: I (132 post-transplant days, PTD), II (160PTD), III (209PTD) and IV (265PTD). These samples were analyzed by ICP-Spectroscopy. The ripening stage affected the Al, Cu and Zn contents in ripe peppers while As presented the highest content in ripening peppers. Harvests I y III presented the highest Al, Ca, K contents while harvests II y III presented the highest As and Pb contents. Nine and ten elements developed authenticity markers according to the maturation and harvest number, respectively. The results obtained will help the producers and industrialists to focused on the production and agronomic management of high quality habanero peppers.