The apple is one of the most important fruit species in the world. Turkey has a diverse and ancient apple germplasm that have played a major role in the domestication of the Malus genus. However, so far locally grown Anatolian apple germplasm has largely been uncharacterized. In this study, 171 local apple (M. domestica Borkh.) accessions originated from eco-geographically diverse regions of Anatolia were studied using 16 SSR (simple sequence repeat) loci, which generated 254 alleles. Of the SSR markers used, the CH04g10 locus showed the highest allele diversity. Relatively high genetic similarities were found between some accessions. The factorial correspondence analysis did not clearly separate different all apple accession groups, suggesting that Anatolian apple accessions are highly intermixed. However, most apple accessions were grouped according to their collection sites in structure analyses. In addition, reflecting the richness of the Anatolian apple germplasm, low numbers of synonymous, and identical accessions were identified among the germplasm. Finally, using the publically available SSR data generated in other studies, we investigated genetic relationships between Anatolian accession groups and European apple accession groups. Our results reported here provide a useful base for future studies aimed at investigating the genetic diversity of wild and cultivated apples from Anatolia and the surrounding regions.