The apricot breeding of Hungary has a long tradition, because its roots go back as early as the 15th century. The various cultivars mainly originated from Mid Asia have given a very good basic material for the domestic apricot cultivation. Our major goal is to set a molecular fingerprint based on molecular markers that will be able to identify certain varieties from an unknown plant material. More than 150 cultivars were selected from different germplasm collection located in Central Europe and finally 96 of them were chosen. The first markers of choice were the isozymes. The corresponding literature showed that these type of markers have been used to assess genetic variability in apricots. However isozyme analysis doesn't detect enough polymorphism to discriminate Hungarian cultivars and reveal relationships among them. The availability of DNA-based markers provides a new possibility for evaluating differences among plant genomes. Simple sequence repeats (SSR and microsatellites) have become the tool for identification in many plant species, because they are PCR-based, highly reproducible, polymorphic and codominant in plant genomes. In this study, we used peach and apricot primer pairs from four different sources for cross species amplification in apricot in order to examine microsatellite polymorphism among cultivars and investigate relationships among them.