Mandarin (Citrus reticulate Blanco) and lemon (C. limon L.) are among the most cultivated Citrus species in the world.Among different approaches, gamma radiation is widely used to induce mutations in citrus breeding studies. Gamma radiation causes DNA damage, randomly inducing several mutations in the genome. Molecular techniquesarewidely used to detect such induced mutations and genetic diversity in plants.In this study, simple sequence repeats (SSR), inter-simple sequence repeat (ISSR) and single-strand conformation polymorphism (SSCP) markers were used to detectthe induced mutations andgenetic diversityin someirradiated mandarin and lemon genotypes in comparison with standard citrus varieties. The irradiated genotypes used in this study derived from populationsthat had been originally obtained with gamma radiation with different gray doses applied on Yerli Mandarin and Antalya YerliYuvarlak lemon varieties. Out of 82 primers (22 SSCP, 30 ISSR and 30 SSR) tested, 55 primers (9 SSCP, 24 ISSR and 22 SSR primers) successfully amplified a total number of 363 amplicons.A single band with an approximate size of 500 nucleotides was determined using the primer ISSR 868 as differentiating between seedy parent and irradiated seedless mandarin genotypes. The polymorphism information content (PIC) values of SSCP, ISSR, and SSR markers ranged from 0.61-0.99, 0.31-0.96, and 0.33-0.96, respectively. Cluster analysis classified lemons and mandarins into 2 subgroups as mutant and commercial lemon genotypes. ISSR markers were found to be more effective to determine the genetic differences among the varieties in comparison to SSCP and SSR markers. The results clearly showed that SSCP, SSR and ISSR markers are important tools to distinguish mutant genotypes andconfirmed their usefulness for phylogenetic studies.