In this study, ‘Ak Sakı’ and ‘Kara Sakı’ apple cultivars were collected from different locations in Erzincan province, Türkiye, and genetic diversity was determined using the Start Codon Targeted (SCoT) marker technique. The SCoT marker technique was chosen because its gene targeting, long primer, and high annealing temperature make it more effective than other marker techniques. Using ten SCoT primers, 60 bands were obtained, and 42 of them were polymorphic. The polymorphism rate was determined to be 70%. The UPGMA (Unweighted Pair Group Method with Arithmetic mean) dendrogram created using the PAUP 4.0b10 program consists of two clades. The genetic distance between apple cultivars varies between 0.13462 and 0.45614. Principal Component Analysis (PCA) results were compatible with the UPGMA dendrogram. With the SCoT marker technique, genetic diversity among apple cultivars can be determined in a shorter time and with more reliable results.