Vanilla planifolia, a highly prized tropical crop, produces commercial vanilla. We investigated RAPD genetic diversity and geographical structure within V. planifolia. Multivariate analyses revealed three separate geographical groups of V. planifolia: a) a Costa Rican group; b) a Mexican group consisting only of cultivated plants from north of the Trans-Mexican Volcanic Belt; and c) a Mexican group from Oaxaca, Chiapas, and Quintana Roo, which are wild and wild-sourced cultivated plants. It appears likely that human action has resulted in movement of northern Mexican plants into the region south of the Volcanic Belt. When supposed translocants are included, a significantly higher genetic diversity is observed south of the Volcanic Belt compared to northern Mexico. Furthermore, cultivar names used in V. planifolia do not appear to reflect genetically defined groups.