The Lowland Mayan culture has been one of the most successful in Mesoamerica. Being an agricultural society, part of their success was based on plant genetic resources which satisfied their needs of social reproduction. This article reviews recent evidence on early agriculture in the geographic area where Lowland Maya culture originated, and discusses its implications for the study of plant domestication and evolution under human selection within this cultural sub-area. Questions of interest for future research are posed. As working hypotheses, we list two categories of species possibly implicated in the origin of this civilization: (1) native species that could have been the subject of local human selection or to some degree of agricultural manipulation by 3400 b.c., and (2) species that could have been introduced from other cultural areas of America by 3400 b.c. and subsequently subjected to local human selection.