Turkey is the second largest producer of watermelon in the world and a considerable number of local cultivars and ecotypes exist in the different regions of Turkey. Twelve peroxidase gene (POX) specific primers developed from the rice genome were used to detect peroxidase gene polymorphism (POGP) in 259 watermelon lines available in the Turkish genetic resources. Cluster analysis indicated that species based clustering and geographical origin of the genotypes were not significant in the clustering. Principle component analysis (PCA) revealed similar results and created three different clusters. The first three Eigen value was calculated and found to be 58.1, which explains the 58% of the total variation. Analysis of molecular variance (AMOVA) indicated 38.56 % variation among the groups, 7.39% variation between populations and within the groups and 54% variation within the population. The genetic polymorphism rate was found to be considerably high in the genotypes studied (98.2%). When both POGP and SRAP markers were considered, Cophenetic Correlation Coefficient obtained by Mantel's Matrix Correspondence Test was found to be r = 0.91, which indicates significant correlation between POGP- and SRAP-based similarity matrices. Considering the polymorphism level and cophenetic correlation between SRAP and POGP markers, POGP markers can be useful in evaluating genetic variation in watermelon genotypes.