Use of molecular markers has been successful at genetic diversity studies of grasses. Plains bristlegrass (Setaria macrostachya Kunth) is a native grass with good forage value in Mexico; however, due to inadequate grazing practices its populations have been decreased. In this study, genotypic diversity of plains bristlegrass populations was explored and characterized in Chihuahua grasslands. Analysis of genetic diversity was estimated with amplified fragment length polymorphism (AFLP) with four pairs of primers. With the banding pattern a binary matrix of presence and absence of bands was made. Molecular data were analyzed using the Statistical Package NTSYSpc. Results showed 186 bands, the 56.45% (105 bands) exhibited polymorphism and 43.55% (81 bands) monomorphism. Polymorphic bands number was 44, 36, 40 and 42 for different combinations of primers EcoRI-AAG+MseI-CTG, EcoRI-ACT+MseI-CTG, EcoRI-AGG+MseI-CAG, and EcoRI-AAC+MseI-CAG, respectively. Monomorphic fragments for these same combinations were 5 for EcoRI-AAG+MseI-CTG, 12 for EcoRI-ACT+MseI-CTG, 3 for EcoRI-AGG+MseI-CAG and 4 for EcoRI-AAC+MseI-CAG. The highest percentage of polymorphism (93%) and polymorphic bands (40) was obtained with the combination of EcoRI-AGG+MseI-CAG primer. Cluster analysis, using Dice coefficient, distinguished four groups. Group I included 33 populations, group II included eight populations, group III joined only one population, and finally the group IV comprised two populations. Ecotypes with high forage potential, based on genetic variability, were 308, 507 and 252). These results are the foundation to start genetic programs on this important forage grass.
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