In Croatia, sour cherry is grown in two production areas: the northern continental and in Mediterranean part. There are many varieties of sour cherry but only the best ones with highest quality are used in production. The common problem of cultivar identification is also burdened by the fact that some varieties have multiple names (synonyms), as well as that often happens that one name is used for more different genotypes, phenomena called homonymy. Until recently, identification was carried out by measurement of morphological and physiological characteristics, but nowadays it is combined with genetic fingerprinting whose results are more reliable. This is the reason for application of microsatellite markers (SSR) in this research which are suitable for fast and reliable variety identification due to their independency of environmental factors. The aim of this study was to examine the possibility of amplification and detection of different SSR markers developed for genus Prunus, all for the purpose of identifying sour cherry varieties from the South East European region. Moreover, the aim was to determine the minimum set of polymorphic loci that can separate all analyzed genotypes and also to create a database of sour cherry SSR profiles. Six SSR markers that were used to genotype 24 sour cherry accessions (19 cultivars, one of them being represented by six clones) successfully amplified and distinguished all 19 cultivars except of six clones of 'Oblačinska' sour cherry thus confirming their suitability for cultivar identification. The selected set of markers proved to be very informative and detected a high level of polymorphism. The most polymorphic loci were BPPCT 26 and BPPCT 34 which can also be considered as a minimum set of markers sufficient for identification in this study because they were sufficiently polymorphic to separate all analyzed cultivars. Also, genetic profiles of six analyzed clones were identical and as expected, showed no variability. Non-redundant table of genetic profiles represents the core database that can be used for further identification of sour cherry germplasm and for research of the origin of sour cherry varieties.