Sennaobtusifolia(L.) is a plant in the genusSennathat contributes to improving nutritional quality, food security, and better health protection for rural populations. However, very few studies have been devoted to it in Burkina Faso. Consequently, its genetic diversity remains poorly known. Such neglect would lead to the erosion of its genetic resource. The general objective of this study is to contribute to a better knowledge of the genetic diversity of the species in order to be able to issue scientific bases for its conservation, valorization, and genetic improvement. Sixty (60) accessions ofSenna obtusifoliawere collected in the wild from five provinces of three climatic zones of Burkina Faso. Molecular characterization was carried out using 18 SSR markers. Fifteen were polymorphic microsatellite markers leading one hundred and one (101) alleles in total, with an average of seven (7) alleles per locus. The number of effective alleles was 2.33. Expected heterozygosity, Shannon diversity index, and polymorphism information content averaged 0.47, 1.05, and 0.47. Molecular characterization revealed the existence of genetic diversity within the collection. This diversity has been structured into three genetic groups. Genetic group 3 presents the highest genetic diversity parameters.