Pearl millet [Pennisetum glaucum (L.) R. Br.] is a food cereal of limited importance in Benin. The conservation and exploitation of these resources are important for the food security of the populations involved in its production. Understanding the structure of its genetic diversity and identification on a molecular basis is an important goal for the support, preservation, and success of breeding programs. In this study, 42 varieties of millet collected in four agro-ecological zones of Benin already grouped into 3 morphological classes were evaluated using 12 microsatellite markers (SSRs). The analysis of the loci revealed a high level of polymorphism (100%), which detected a relatively large number of alleles (A=52) for an average of 4.3 per locus. Means of PIC, observed heterozygosity (Ho) and gene diversity (He) are respectively 0.63, 0.58 and 0.64. Typology of varieties by the UPGMA method using the SAHN procedure and the Principal Coordinate Analysis (PCoA) based on genetic distances showed the existence of three major genetic groups. The analysis of these results shows that farmers' practices have an impact on the genetic structuring of millet in Benin
