In this study, it was aimed to determine the quality, phytochemical contents and molecular characterization of the best thirteen pomegranate genotypes selected as a result of the selection study carried out between 2019-2020 in the İnhisar district of Bilecik province. As a result of the research, the fruit weight of the selected promising genotypes and cultivars was between 208.00 and 601.3 g, fruit width was 74.54-103.47 mm, fruit length was 63.08-92.32 mm, hundred-aril weight was 28.00-66.25 g, aril yield was determined as 35.48-85.00%. The amount of soluble solid was determined between 14.33 and 18.77%, while pH values were between 3.22 and 4.36% and titratable acidity was between 0.23 and 1.72%. The total antioxidant capacity, which was determined with the TEAC method, was 3.28-8.48 µmol TE g-1, while the total amount of phenolic substances was 956.10-2116.10 g GAE kg−1, and the total amount of anthocyanins was 45.50-344 µg Plg-3-glu/g. Seven UBC-ISSR primers were employed to conduct molecular analyses aiming to determine polymorphism levels among the selected thirteen genotypes, along with the comparative Fellahyemez, Katırbaşı, and Hicaznar varieties. The resulting dendrogram is divided into two main clusters at a 25% dissimilarity level, one smaller and the other larger. All local genotypes clustered within the larger group, with Genotype 9 and Genotype 10 exhibiting the closest similarity. When the criteria determined as a result of the study were examined, it was determined that among the selected pomegranate genotypes, there were individuals that could be registered as table and industrial.