The ecological success of lichens is related to both myco- and photobionts which condition the physiological limits of the lichen symbioses and thus affect their ecological niches and geographic ranges. A particular type of lichen, called cephalolichen, is characterized by housing both green algal and cyanobacterial symbionts—the latter is restricted to special structures called cephalodia. In this type of lichen, questions related to specialization within species or within individuals are still unsolved as different patterns have previously been observed. In order to study the variability at the intrathalline, intraspecific, and interspecific level, cyanobionts from different cephalodia within the same thalli and from different thalli were genetically analysed in three cephalolichen species at two different forests (18 thalli, 90 cephalodia). The results showed variability in the cephalodial Nostoc OTUs in all the studied species, both at the intrathalline and intraspecific levels. The variability of Nostoc OTUs found in different cephalodia of the same thallus suggests low specialization in this relationship. Additionally, differences in OTU diversity in the three studied species and in the two forests were found. The variability observed may confer an increased ecological plasticity and an advantage to colonize or persist under additional or novel habitats or conditions.