Background: In recent years, DNA-based markers have been used quite extensively because of their many advantages over the traditional morphological and biochemical markers. Many studies have shown that molecular markers are useful in delineating the genetic relationships among closely related mulberry genotypes and cultivars. Thus, in the present study, polymer chain reaction based DNA fingerprinting techniques were used to investigate the genetic relationships among mulberry genotypes growing in different agro-climatic regions of Turkey. Results: 20 RAPD primers generated a total of 173 bands, of which 157 (90.75%) were polymorphic. As for 11 ISSR primers, 124 bands (96.55%) were polymorphic in a total of 128. The similarity index for RAPD technique ranged between 0.24-0.98; 25Is203 with 25Is112 were found to be the closest genotypes, while 24Ke10 and 25Is123 were the most distant ones. According to the ISSR result, the genetic similarity index changed between 0.21-095; 25Is203 with 25Is112 genotypes were the closest, while 25Is08 and 01KaD2 were the most distant ones. Conclusion: The RAPD and ISSR markers were found to be promising for assessing genetic diversity in mulberry genotypes. © 2011 Society of Chemical Industry.