Turkey has many valuable genetic resources for pomegranate; however, there have not been many studies on the identification and characterization of these important genetic resources. New microsatellite markers were used to characterize a set of 78 pomegranate accessions from Turkey. Using six SSR primers, a total of 41 alleles were characterized with an average of 4.6 alleles per locus and mean probability of identity (PI) value of 0.366. These data indicated a high level of polymorphism in pomegranate germplasm. Five synonymous groups could be detected among 30 accessions. This microsatellite-based key is a first step towards a database for marker-assisted identification of pomegranate accessions in Turkey. The present study provides essential information to devise a pomegranate core germplasm collection without duplication of plant material, to sustainably manage pomegranate breeding programs, and to establish conservation strategies for preserving local pomegranate genetic resources.