Genetic diversity in maize and its wild relative teosinte ( Zea mays ssp. mexicana) in Mexico is important for the sustainability and improvement of the third most important crop in the world. This study examines the genetic diversity of sympatric and allopatric populations of maize and teosinte and evidence for hybridization in Mexico using isozyme electrophoresis. We take a population level approach to the analysis of genetic diversity in standing Mexican populations. Our data provides evidence that hybridization contributes to the genetic similarity between sympatric pairs of maize and teosinte populations compared with allopatric populations of either subspecies. Introgressed populations of teosinte show an increase in diversity relative to isolated populations. To date, introgression from teosinte does not appear to play an important role in the genetic diversity of sympatric maize. Patterns of differentiation among sympatric and allopatric populations of maize and teosinte indicate that introgression occurs more often than previously thought. Additionally, recent introgression between maize and teosinte has resulted in morphological hybrids that often have genetically transgressed allele frequencies compared to adjacent maize and teosinte populations.