An understanding of Mesoamerican agricultural origins is hampered by the fact that few archaeological sites pertinent to the question have been explored. The Guilá Naquitz site in southern Mexico has some of the earliest evidence for the shift to food production in Mesoamerica, including extensive evidence for the use of acorn (Quercus species), piñon pine nut (Pinus edulis), prickly pear (Opuntia species), mesquite seeds (Prosopis species), wild runner bean, and the seeds of various grasses. Several squash seeds that are larger than those from wild squashes have also been found at this site, indicating that domestication was occurring. One of the largest of these seeds has been directly dated to 10,000 bp, making it among the oldest evidence for a domesticated plant in the Americas. Local experimentation with foxtail grass seems to have led to a failed domestication attempt. Pollen from domesticated corn and manioc has been found in levels dating to 7000–6000 bp at the San Andrés site in the gulf coast of Tabasco, Mexico. Cotton pollen and seeds that may be from the domesticated sunflower (Helianthus species) have also been recovered there and dated to 4600 bp. However, the sunflower is problematic because all available evidence is for its domestication in eastern North America, suggesting that the Mexican specimens may belong to another species. Low-density, highly mobile Preceramic populations were responsible for these developments.

Despite the prominence of corn in the late archaeological record of Mesoamerica, the origins of this crop are still not clearly understood. It is likely that corn was first domesticated by native peoples in southern Mexico about 10,000 years ago. The oldest recovered corn cob is from Guilá Naquitz and dates to between 6300 and 6000 bp. Among the wild grasses—including teosintes (e.g., Zea diploperennis and Z. mays parviglumis), the best candidates for the wild ancestor of corn—none have the extraordinarily robust and productive cob structure of corn. In one model a series of massive mutations has been proposed to account for the development of the corn cob, but how to account for these mutations is problematic. Instead of requiring mutations, a recent genetic analysis indicates that a third grass, gamma grass (Tripsacum dactyloides), crossed with teosinte to produce a hybrid with the cob structure typical of corn. Although teosinte is not particularly palatable, Tripsacum has a history of being used for food. People may have recognized teosinte-Tripsacum crosses in the wild and selected them for planting. Another possibility is that teosinte and early corn were exploited first for the sugar content of their stalks and leaves. Ancient Mexicans chewed the leaves and stalks of early corn for their sweet flavor, and the sugar and starch from corn were also useful in making alcohol, an important comestible in many types of social interactions. Corn kernels would have been less important in these contexts, making it less likely that they would be preserved. This might help explain the rarity of corn in the early archaeological record. Whatever its origins, corn became a staple crop of the Americas, where it was often prepared as a potage or by boiling in limewater and grinding. Cornmeal paste was then made into tortillas, flat cakes, or gruel.

Villages did not become common in the Americas until the so-called Early Formative period, which began about 3800 bp, after corn was domesticated. Village life was based on the extended family, composed of parents and their children’s families, which provided the labor force. Villages were organized into larger territorial units based on ceremonial centers that commonly featured flat-topped pyramids. Eventually, Formative groups such as the Olmec, known for carving colossal stone heads, developed large prosperous towns. Larger territorial units developed about 2000 bp, and Formative cultures were eventually eclipsed by the Maya, Toltec, and Aztec empires. Food was supplied to these empires’ large urban centers by a combination of rain-fed swidden fields and gardens and irrigated tropical lowland field systems.

Prominent crops in Mesoamerica eventually included avocados, cacao, chili peppers, cotton, common beans, lima beans, corn, manioc, and tomatoes. . The principal domestic animals were the turkey, dog, and Muscovy duck. Irrigation, terracing, and the use of artificial islands (chinampas) increased land usage in areas with less precipitation. The land was cleared by chopping and burning, and the seeds were sown with the aid of fire-hardened digging sticks. Crops were stored in pits or granaries. It is apparent that much remains to be learned about early agriculture in the Mesoamerican lowlands.