In Hizan province of Turkey, which is located in the central east of the country, hazelnut farming is performed by almost 400 families in 15 villages. Here, we report on genetic diversity and several nut characteristics of Hizan hazelnuts. Molecular characterization of 28 clones representing the 7 major local landraces called ‘Beynane’ (the most preferred landraces by the local market), ‘Çavraş’, ‘Gevrik’, ‘Himdi’, ‘Hurişta’, ‘Sevane’, and ‘Turşink’ was conducted by the analysis of 11 Simple Sequence Repeat loci. The alleles of Hizan hazelnuts and 14 reference genotypes were also pooled and compared with 145 accessions representing the hazelnut genetic diversity. For the 28 samples, the number of alleles per locus ranged from 2 to 8, with a mean of 3.55. Mean values for expected heterozygosity, observed heterozygosity, and polymorphism information content were high, averaging 0.56, 0.74, and 0.49, respectively. Cluster analysis of Hizan hazelnuts showed that they are distinct and genetically closer to Kayseri hazelnuts rather than main Turkish Black Sea hazelnuts. Mostly clones of landrace grouped together closely on the dendrogram and none of the clones of accessions were found to be genetically identical at 11 loci. Morphological characterization of fruits depicted relatively high variation. Highest nut weight was observed for ‘Beynane’ lone 6 with a mean of 4.69 g and minimum nut weight was observed for the ‘Gevrik’ clone 1 with a mean of 2.07 g. The highest nut length (24.2 mm) and width (21.6 mm) were determined for ‘Beynane’ whereas the minimum nut length (17.6 mm) and width (16.4 mm) were determined for ‘Gevrik’. The results indicated a unique genetic structure of Hizan hazelnut cultivated germplasm and necessity for further studies including detailed molecular characterization and selection of best clones of local accessions.