The use of appropriate grapevine rootstocks is a unique solution for preventing soil-borne problems. As commonly used rootstocks were mostly derived from different North American Puis species, each genotype has specific behavior concerning resistance to biotic and abiotic stress factors. Therefore, reliable characterization of rootstocks provides valuable knowledge to breeders in selecting proper material. In the current study, nineteen grape rootstocks were genotyped with four AFLP (Amplified Fragment Length Polymorphism) primer combinations. A total of 416 bands, of which 357 were polymorphic (86%), were generated while total number of bands per primer combination ranged from 63 to 124 with an average of 104. The pair-wise distance coefficient values were between 0.04 ('Cosmo 10' and 'Cosmo 20') and 0.41 ('Saint George' and 'Cosmo 20'). Certain genotype-specific markers were detected for '41 B' and 'Saint George' rootstocks. A dendrogram constructed from AFLP analysis formed five taxonomic groups relevant to genetic distances of genotypes belonging to certain species. On the other hand, close genetic relationship was found among the Cosmo rootstock group, with 'Cosmo 2' being the most genetically distinct. AFLP primer combinations employed in this study revealed a high degree of polymorphism and therefore, they have proven to be a powerful tool for further analysis of closely related grape genotypes.