The genetic diversity of Turkish watermelon genotypes selected from the watermelon genetic resource collection was evaluated by simple sequence repeat (SSR) and sequence- related amplified polymorphism (SRAP) markers. Most of the accessions were collected from various geographical regions of Turkey. Different Citrullus species, wild relatives, foreign landraces, open pollinated (OP), and commercial hybrid cultivars were also assessed for genetic relatedness. Fourteen SSR primers and 31 SRAP primer combinations were used in the experiment. Both SSR markers (100%) and SRAP markers (97.3%) generated high polymorphisms. Based on the SSR and SRAP data, the genetic similarity coefficients were calculated, and dendrograms were constructed using the unweighted pairgroup method with arithmetic average (UPGMA). Cluster and principle coordinate analyses indicated that Citrullus lanatus var. lanatus subspecies genotypes collected from the different regions of Turkey were closely genetically related. Overall, our results displayed low genetic variability within the Turkish watermelon germplasm in contrast with their high morphological diversity.