Background: The assessment of genetic diversity is an asset for the development of any varietal conservation and improvement strategy. Methods: This work aims to establish the level and structure of genetic diversity of 54 accessions of amaranth collected in two climatic zones (Sudanese zone and Sudano-Sahelian zone) of Burkina Faso. Fourteen (14) ISSRs markers developed by eurofinmwg/ Operon were used in this study. Results: Eight (8) of them were been polymorph and used for data analysis. All eight primers showed 100% polymorphism with an average PIC of 64%. A total of 40 alleles were revealed with an average of 5 alleles by locus. Also, an average of effective allele number of 3.94, a heterozygoty expected of 0.37 and Shannon diversity indexes of 1.3 were recorded. These parameters calculated showed that the markers used are informative and revealed an important genetic variability structured in four groups (A, B, C and D) within the collection amaranth cultivated in Burkina Faso. The influence of "climatic zone" and "morphotype" factors on the level and the organization of genetic diversity is very low. Conclusion: 98.80% of total genetic diversity is due to variability intra-population.

Amaranth, neglected species, molecular variability