This article compares the species and varieties seen and described in the XVI century by the encomenderos of several towns in Yucatán (as well as those that appear in other records, both colonial and current), with the species and varieties found at the end of the 80’s of the last century, particularly in the town of Xocén, in eastern Yucatán. The conclusion is that not only were the phytogenetic resources of the milpa not lost, but after the conquest they were preserved and even enriched with some interesting introductions. Since the milpa was not only used for subsistence, but also produced surpluses that sustained the large pre-colonial populations of the Yucatán Peninsula, we propose several conditions of the time that may have favored its high yields.