Developing successful strategies to ensure future increase in yield of soybean and peanut crops hinges in part, on improving the genetic basis of the cultivars. Knowledge of genetic relationships in crop breeding programs provides valuable information that can be used by plant breeders as a parental line selection tool. So far, a thorough analysis of genetic diversity among the soybean and peanut genotypes grown in Turkey had not been attempted at DNA level. In this study, inter-simple sequence repeats (ISSR) and sequence-related amplified polymorphism (SRAP) markers were used to evaluate the genetic diversity between 21 soybean and 32 peanut cultivars and breeding lines adapted to different regions of Turkey. The ISSR analysis, which was performed with 46 primers in soybean and 47 primers in peanut, yielded 31 and 26 polymorphic bands, respectively, while 26 and 17 polymorphic amplicons were amplified by 34 and 36 SRAP primer combinations in soybean and peanut, respectively. The unweighted pair group method with arithmetic means dendrograms (UPGMA), based on Jaccard similarities,were obtained from the combined ISSR + SRAP data for both soybean and peanut. In soybean, UPGMA dendrogram clustered all soybean cultivars into the same group except 'Yesilsoy', whereas, in peanut, it separated cultivars southwest runner and spantex from all the other cultivars, breeding lines, and plant introductions. In light of the narrow germplasm base of soybean and peanut genotypes grown in Turkey, a renewed emphasis should be placed on the introduction of new sources of germplasm into the breeding pool in order to enhance genetic variability to permit continued progress in developing high yielding cultivars and lead to greater gains for selections. The results obtained from this study will be helpful for soybean and peanut breeders in Turkey to gain information about genetic diversity and will enable them to make a future strategy for broadening the genetic basis of these crops.