The present study was designed to identify intra-varietal diversity via SSR markers within ‘Askari’ and ‘Keshmeshi’ (Vitis vinifera L.). These two semi-seedless grape cultivars are used as table grape and raisin. Some accessions of these cultivars are morphologically different. For instance, some accessions had big berries with big bunches and empty seeds, whereas others had small berries in small bunches with soft seed traces. In order to evaluate these differences in genetic level, we selected 14 SSR loci to evaluate intra-cultivar diversity. In total, 42 accessions of ‘Askari’, 10 accessions of ‘Keshmeshi’ and one accession of Sultanina as a control were analysed, using a capillary electrophoresis fragment sizing system. Genetic analysis discriminated six accessions of ‘Askari’ (No. A3, A21, A31, A44, A46 and A114) which were different from other accessions. These accessions were also different in some morphological traits. Accessions no. A3 and no. A21 had soft seed traces and Berries and bunches were smaller than others. Other accessions had empty seeds. Accessions no. A44, A46 and A114 had big bunches, big berries and empty seeds. In accession no. A31 berry shape was approximately round vs. oval shape in other accessions. The remaining accessions (36 accessions) were identical in 14 SSR loci. In ‘Keshmeshi’ four different accessions (No. K6, K8, K15 and K27) were discriminated in genetic analysis. In accessions no. K6 and no. K8, the number of bunch and yield per vine was more than other accessions. In accessions no. K15 and no. K27, berries and bunches were bigger than others and the number of seed traces was more than other accessions. Other six accessions were identical in14 SSR loci. Cluster analysis of all three cultivars divided accessions to three groups (each cultivar in one group) at 0.67 similarity coefficient. Our study showed SSR markers can be useful for identifying of intra-cultivar diversity.