Conservation of genetic resources is essential for the continuation of future crop production. Watermelon (Citrul-lus lanatus), a member of Cucurbitaceae, is widely distributed in tropical and subtropical regions. The aim of this study was to reveal the genetic relationships with the help of microsatellite markers in a watermelon collection free of unnecessary repetitions, and to determine the success of SSR (Simple Sequence Repeats) primers developed in cucurbits. In this study, 96 watermelon genotypes with good agronomic characteristics were used among the geno types collected from different regions of Turkey and purified up to the S4-S6 (self-pollination) stage. In the study, 33 SSR primer pairs were used to determine the genetic relationship between watermelon genotypes. In the study, a total of 67 bands were obtained with SSR primers. As a result of UPGMA (Unweighted Pair Group Method Using Arithmetic Averages) analysis, genotypes showed similarity at the level of 0.84-1.00. The number of alleles detected per primer varied between 1 and 6. In terms of the total number of alleles obtained, CMCT44 (5 units) and Cgb4767 (6 units) loci produced the most alleles. Primers with high polymorphism rate and allele excess were determined, and the possibilities for use in genetic stability analyses, variety differentiation and other genetic analyses were determined.