Sunflower ( Helianthus annuus L.) is used as 'seed snacks' so called 'pipas' in the Mediterranean countries which may offer an interesting opportunity for agricultural diversification of this crop. The morpho-phenological variability already demonstrated in the Tunisian local populations can be a basis for the creation of new varieties well adapted to climate and soil conditions in that region. The molecular characterization of 59 accessions and reference lines generated 194 alleles from 30 SSR loci (3'10 alleles per locus) and 54 haplotypes built from 117 SNP detected by NGS sequencing of 7 genes (4'16 haplotypes per gene). These data highlight some uniqueness of the Tunisian material compared to 7 control lines but a low genetic dispersion between accessions. However a core collection of 8 populations capturing 88 % of the Tunisian genetic diversity could be proposed for a future sunflower breeding program.