Turkey has a diverse apple germplasm and Northeastern Anatolia had great contributions to domestication of the Malus genus. Despite quite high rainfall (900–2300 mm) and humidity (70–85%) levels, several local apple cultivars have been successfully grown for centuries at the coastal zone of Eastern Black Sea region of Northeastern Anatolia without any pesticide applications. In this study, a set of 206 local genotypes, including 6 international cultivars as references was analyzed using 13 SSR primers with the aim of assessing the genetic diversity and population structure among the genotypes. Bayesian genetic structure analysis was used to reveal differentiation of the groups and the results were confirmed by factorial correspondence analysis (FCA). A total of 234 alleles (average 18) were generated by 13 SSR markers. CH02c06 was the most informative (PI: 0.017) and CH03g07 was the least informative (PI: 0.07) locus. The average He was 0.859 with a range of 0.775–0.929 and the average Ho was 0.760 with a range of 0.556–0.872. Considerable genetic variation was detected among the genotypes and genetic similarity varied between 11 and 96%. A Bayesian genetic structure analysis indicated three subpopulations (K) and admixture among the accessions. Several loci yielded three alleles in 39 accessions. No synonyms or identical cultivars were detected but several genotypes known by the same names formed 22 homonym groups. The present SSR data will have great contributions to future germplasm management efforts as well as to further comparative studies that investigate genetic relationships among the local apples of Northeastern Anatolia.