Abstract: Data on molecular markers, anthocyanin contents and antioxidant activities are increasingly used in breeding programs of many horticultural crops. Inter simple sequence repeat (ISSR) analysis, anthocyanin contents and antioxidant activities were used to characterize 10 strawberry (Fragaria x ananassa Duch.) cultivars and nine breeding lines. Fifteen primers generated 240 polymorphic ISSR-PCR bands. Cluster analysis by the unweighted pair-group method with arithmetic averages (UPGMA) revealed a substantial degree of genetic similarity among the genotypes ranging from 45% to 73% that were in agreement with the principal coordinate (PCO) analysis. Wide genetic diversity was observed among the strawberry genotypes for anthocyanin contents and antioxidant activities. The ISSR analysis together with data for antioxidant activities and anthocyanin contents in strawberries could be used for germplasm management and more efficient choices of parents in current strawberry breeding programs.