Observed levels of population genetic diversity are often associated with differences in species dispersal and reproductive strategies. In symbiotic organisms, the genetic diversity level of each biont should also be highly influenced by biont transmission. In this study, we evaluated the influence of the reproductive strategies of cyanolichen species on the current levels of population genetic diversity of bionts. To eliminate any phylogenetic noise, we selected two closely related species within the genus Degelia, which only differ in their reproductive systems. We sampled all known populations of both species in central Spain and genotyped the fungal and cyanobacterial components of lichen samples using DNA sequences as molecular markers. We applied population genetics approaches to evaluate the genetic diversity and population genetic structure of the symbiotic components of both lichen species. Our results indicate that fungal and cyanobiont genetic diversity is highly influenced by the reproductive systems of lichen fungus. We detected higher bionts genetic diversity values in the sexual species Degelia plumbea. By contrast, the levels of fungal and cyanobiont genetic diversity in the asexual species Degelia atlantica were extremely low (almost clonal), and the species shows a high specificity towards its cyanobiont. Our results indicate that reproduction by vegetative propagules, in species of the genus Degelia, favors vertical transmission and clonality, which affects the species' capacity for resources and competition, thereby limiting the species to restricted niches.