SSR analysis of chloroplast and mitochondrial genomes of cultivar lines and wild species of sunflower (Helianthus L.) were completed. The polymorphism of 18 microsatellite loci of the chloroplast and mitochondrial genomes was investigated. Based on the obtained data was constructed dendrogram showing the genetic diversity of chloroplast and mitochondrial genomes of sunflowers. The studied species were clustered into annual and perennial. This set of novel polymorphic SSR markers can be useful for breeders and molecular biologists for the genetic diversity analysis, lines identification and improve breeding.