We investigated the possible utility of randomly amplified polymorphic DNA (RAPD) markers in our lemon (Citrus limon Burm. F.) breeding program emphasizing the excellent quality and tolerance to mal secco disease caused by Phoma tracheiphila Kanc. et Ghik. The genotypes studied included 12 advanced selections that were previously shown to be resistant or tolerant to this disease and 4 lemon varieties ("Kutdiken 79", "Tuzcu 05-Yediveren Kutdiken"; "Finike Yerli Yuvarlak", "Antalya Yerli Yuvarlak"). DNA characterized the 16 lemon genotypes. We scored 350 bands generated by 48 selected RAPD primers. 38.85% of these were constant corresponding to monomorphic loci while 61.14% of the bands were polymorphic. The number of bands for each primer varied from 2 to 15 with an average of 7.3 bands per primer, the sizes of the amplified DNA bands ranged from 250 to 3000 bp. Primers differed in their capacity to detect polymorphism and total proportion of polymorphic products ranged from 12.5% to 100%. The analysis of 16 lemon genotypes using 48 RAPD primers allowed us to distinguish all genotypes except "Tuzcu 896" and "Tuzcu 897" which were selection of "Tuzcu 9N Aklimon". The dendrogram indicated that the genotypes can be separated into two major groups with a similarity value of 0.79. These results show that utilization of RAPDs can offer great benefits to our lemon breeding program in several ways. such as identifying genotypes and studying the genetic similarity among genotypes. The future work can be extended to develop RAPD markers linked to gene(s) conferring tolerance to mal secco.