Turkey has more than 4 million walnut trees (Juglans regia L.), most of which are derived from seedlings, and are nongrafted trees. This characteristic leads to a huge opportunity to select superior walnut genotypes from natural populations for cultivation and for breeding programs. Several selection studies have been performed in the last decades and few genotypes were selected. The goal of this study was to characterize and determine genetic relationships among 21 walnut genotypes with potential in walnut production using amplified fragment length polymorphism (AFLP) and selective amplification of microsatellite polymorphic loci (SAMPL) techniques. Eight primer combinations (six for AFLP and two for SAMPL) were applied to 21 walnut genotypes and a total of 230 bands of which 50.4% of them were polymorphic were obtained. The SAMPL technique was more effective than AFLP in the separation of very closely related genotypes. Genotypes of the pairs 'Maras-18'with 'Maras-46', 'KSU-5'with 'Sutyemez-1', 'Maras-12' with 'Sutyemez-2,"Kaman-3' with 'Kaman-4', and 'KSU-11'with 'Maras-10' were the most closely related.