Polyembryony is a trait widely distributed in nature which occurs in different plant species including maize. This trait has been studied at the genetic level with various molecular markers. In the present study we analyzed two monoembryonic and polyembryonic maize groups, derived from the F2 population of a cross between plants from a high polyembryonic brachytic (BAP) population and a monoembryonic commercial variety (PUMA). Polymorphism was analyzed among and between these two F2 maize groups with AFLPs (amplified fragment length polymorphisms). A total of 16 polymorphic bands were obtained, which were recorded as binary code (1 for band presence and 0 for absence). The data were analyzed using the InfoGen software. Contingency of AFLP against polyembryony was determined using the Chi square association. The results suggest a low genetic diversity between the F2 groups. This result was corroborated with the Chi square test which indicated that two markers (13 and 15) may be related to polyembryony. The present study is the first report using segregating populations to identify more than one locus associated with PE in maize by marker techniques.