Myrtle is known native to Southern Europe and North Africa and was naturally grown in tropical and subtropical regions. Myrtle could be grown successfully in soils under hot, arid environments. Myrtle has several genotypes with yellowish-white or bluish-black colored fruits. The present study aimed to investigate genetic diversity among myrtle genotypes with different fruit colors from different parts of Turkey. A total of 28 myrtle genotypes were collected from Adana, Mersin, Hatay provinces of Turkey. 19 ISSR primers were used for the characterization of the 28 myrtle genotypes. In total, 19 ISSR primers produced 99 clear and reproducible DNA band profiles, 89 of which were polymorphic. Therefore, the average polymorphic was 89.90%. In conclusion, we determined that the ISSR molecular markers could differentiate the white and dark-fruited myrtle genotypes. Myrtle genotypes were also separated according to their geographical origin.