Single Nucleotide Polymorphisms (SNPs) provide an important tool for cultivar identification in studies of genetic diversity, but until now the time consuming and costly nature of DNA sequencing has limited the identification of new markers. Herein, we describe the application of High-Resolution-Melting (HRM), a recent enhancement to traditional DNA melting analysis for the characterization of polymerase chain reaction products and the identification of nine gene based SNPs for distinguishing the main Greek sweet cherry cultivars. Expected heterozygosity value of nine SNPs averaged at 0.518. The combined power of discrimination for the SNP markers was 0.999969. The ability of HRM to accurately discern nucleotide changes in a DNA sequence makes it a cost- and time-effective alternative to traditional sequencing for the detection of gene based SNPs.