© 2022, The Author(s), under exclusive licence to Springer Nature B.V.Garlic is a vegetable widely used both in food and as a pharmaceutical raw material in the world due to its contents. Although morphological differences are observed in garlic, which is obligatory apomictically propagated, clonal propagation causes narrowing variation, a genetic bottleneck. This situation complicates breeding programs aiming improvements in preferred agronomic characteristics. For this reason, determining the morphological and molecular differences between garlic genotypes originating from Turkey is important for breeding studies. In this study, morphological and molecular characteristics of 39 garlic genotypes, which are widely cultivated in Turkey, were determined. Kahramanmaraş4 genotype was different from other genotypes in terms of some morphological features (fresh weight, dry weight, and bulb diameter). In the molecular characterization study, 10 Inter-Simple Sequence Repeats (ISSR) primers were used, and it was determined that the genotype TekDiş31 of Tunceli region was different from other garlic genotypes. Genetic similarity coefficient was found to be high (0.85–1.0) in genotypes except for TekDiş31 garlic genotype. In general, some garlic clones (Maraş3 and Kayseri30, Urfa33 and Topaklı35, Kastamonu22 and Kastamonu28, Urfa10 and Kastamonu14, Kastamonu29 and Bademci23) were completely similar to each other, while few differences were found among others. In conclusion, this study revealed that the garlic plant, despite its clonal propagation, consisted of some level of morphological and partially molecular variation. Due to its mode of reproduction (vegetative), this variation may largely be due to point or chromosomal mutation. Furthermore, the 10 identified ISSR primers can generate valuable information for genetic diversity for use by garlic breeders.