Apple (Malus domestica Borkh.) is one of the most economically important pome fruits worldwide and Turkey is within origin center of apple. In this research, inter-simple sequence repeat (ISSR) markers were used to determine relationships among the Turkish apple accessions and some selected foreign cultivars and species. Fourteen ISSR primers produced a total of 111 fragments and 76 of them were polymorphic. The number of average polymorphic fragments per primer was 5.4. The mean polymorphism information content (PIC) was 0.37. The unweighted pair group method arithmetic average (UPGMA) analysis demonstrated that the accessions had a similarity range from 0.79 to 0.98. All accessions studied were discriminated and many subgroups were determined in the dendrogram based on the UPGMA analysis. High level of variation among the Turkish apples existed. Foreign cultivars, M. baccata, M. prunifolia and M. sylvestris accessions studied mix-clustered among the Turkish accessions. For sub-structuring Bayesian analysis, 71 loosely or uncorrelated markers with less than 10% missing data were used. This indicated absence of subpopulations, meaning well and equal introgression of genetic backgrounds or species available among the accessions. It can be concluded that Turkey was rich in apple genetic diversity, which may provide opportunities for apple breedind programs.