The study of the genetic diversity of cultivated plants is an important activity, contributing to the conservation of genetic resources and also to the selection of genetically diverse parent lines from several genetic populations. The aim of this study is to contribute to a better knowledge of the genetic diversity of amaranth grown in Burkina Faso. Eleven microsatellite markers (SSR) were used to genotype 72 amaranth accessions. The markers tested proved to be 100% polymorphic and generated a total of 35 alleles, with an average of 3.27 alleles per marker. The frequency of observed heterozygosity averaged 0.26 per locus and was slightly lower than the expected heterozygosity (He=0.27). Axis 1 and 2 of the PCoA explained 39.27% of the population distribution variance. The analysis of variance showed that there was only 2% variation between morphotypes. The degrees of genetic differentiation Fst calculated between the morphotypes were low (0.05 ≤Fst≤0.11) showing numerous genetic exchanges between these morphotypes with the exception of the dark green morphotype where gene flow (0.286 ≤Fst ≤0.452) was low with the other morphotypes. The genetic distance between pairs of climatic zones indicates a very small distance (0.04) between Sahelian and Sudano-Sahelian zones. Genetic structuring using STRUCTURE 2.3.4 software and Darwin version 5.0.155 software showed no morphological or genetic distinction, indicating little genetic divergence between the groups. These preliminary results show that the population studied has satisfactory genetic diversity, which can be used as a basis to guide conservation and sustainable breeding programs for amaranth in Burkina Faso

Keywords: Amaranthus, microsatellites markers, morphotypes, phylogenetic, genetic variability