Among fruit species cultivated in Turkey, quince shows a great deal of morphological variability and adaptability to the various environments. We attempted to study genetic relationships among 40 quince accessions using amplified fragment length polymorphisms (AFLPs) for future breeding programs. The accessions were previously characterized based on their pomological and yield characteristics and then the best ones were planted in a single collection in Ataturk Central Horticultural Research Institute, Yalova, Turkey. Six AFLP primer combinations generated a total of 746 bands, 493 of which were polymorphic (66.1%). Resolving powers of the AFLP primers ranged from 48.0 to 99.6 making a total of 421.5. Unweighted Pair Group Method with Arithmetic Average (UPGMA) clustering of the accessions showed three major clusters and 'SapancaEsme' and 'Esme-3' were the closest accessions with 95% similarity. Our study indicated that there is a high level of genetic diversity among quince accessions in Turkey and the results of this study can be used for future cultivar breeding programs in quince.