Analysis of microsatellite sequences was used for estimation of genetic diversity of cultivated and wild sunflower and usefulness for genotype identification, genetic purity and “hybridity range” definition. In total 13 SSRs were tested. Unique alleles for some wild sunflower species were found. Eight out of 13 SSR loci were polymorphic for the investigated inbred lines. Four of the investigated microsatellites are suitable and sufficient for genome identification and determination of parentage of hybrids. A procedure is proposed for sunflower genotype registration based on DNA-typing.