The objective of this research was the molecular and phylogenetic characterization of local maize populations of the La Sepultura Biosphere Reserve (REBISE), Mexico. In nine communities from the REBISE, Mexico, nineteen populations of local maize were sampled during 2012-2013. Two improved commercial varieties (Vs-536 and V-424), a commercial hybrid (H-MX3), a local corn (Coastal) recently introduced in the REBISE, two local materials from the state of Tlaxcala, Mexico; both from Chalqueño race and conical Elotes (young corns) and a teosinte (Zea mays ssp. Mexicana) were included. They totaled twenty six different samples. The characterization was done with the PCR technique and inter-type microsatellite genetic markers. In total 113, fragments were ampli ed and that ranged from 150-2200 bp, of which 85,8% were polymorphic. Sequences “AG”, “AC” and “GAA” showed a greater number of ampli ed bands and higher polymorphism. The primers comprised of UBC834, I9 and UBC868 ampli ed the best. The similarities found within the polymorphic bands may be due to their equality such as varieties, races, species or genetic combination effect, a result of their cross- pollination. The dendrogram obtained showed a relatively low cophenetic correlation (r= 0,721), with a low degree of reliability, however four major groups of varieties are clearly conformed. The first was named Valles Altos Corns, integrated by the conical Chalqueño and the conical Elotes races; the second is identified as having a common ancestor with Teocintle; the third is an improved hybrid by the H-MX3; and the fourth includes the REBISE local maize varieties and other commercial varieties (Vs-536 y Vs-424). 

Keywords: protected areas, ISSR, polymorphism, genetic variability.