Randomly amplified polymorphic DNA (RAPD) and inter simple sequence repeat (ISSR) methods were used for investigating genetic variation within L. radiosa and for delimiting species within the genus Lobothallia. Ten RAPD and 11 ISSR primers produced a total of 261 and 260 reproducible bands, respectively, and all of which were polymorphic for the two markers, suggesting high genetic variability within L. radiosa. Genetic distances between the samples of L. radiosa for the RAPD and ISSR analyses ranged from 51 to 93% and from 56 to 92%, respectively. The average was 71.2% for the RAPD markers while it was 80.4% for the ISSR markers. Although a high number of sample-specific bands (31 for RAPD and 16 for ISSR) were seen in L. radiosa, no species-specific band was observed. The RAPD-based dendrogram clustered the samples of L. alphoplaca into one group except for the samples from Kayseri and Nigde, whereas it divided the samples of L. radiosa into two main groups. On the other hand, the ISSR-based dendrogram resulted in four main groups. While the first main group included the three samples of L. alphoplaca, the other three main groups consisted of the samples of L. radiosa. Both RAPD- and ISSR-based dendrograms partially grouped the samples of L. radiosa and L. alphoplaca based on their geographical origins.