Lichens are a well-known symbiosis between a host mycobiont and eukaryote algal or cyanobacterial photobiont partner(s). Recent studies have indicated that terrestrial lichens can also contain other cryptic photobionts that increase the lichens’ ecological fitness in response to varying environmental conditions. Marine lichens live in distinct ecosystems compared with their terrestrial counterparts because of regular submersion in seawater and are much less studied. We performed bacteria 16S and eukaryote 18S rRNA gene metabarcoding surveys to assess total photobiont diversity within the marine lichen Lichina pygmaea (Lightf.) C. Agardh, which is widespread throughout the intertidal zone of Atlantic coastlines. We found that in addition to the established cyanobacterial photobiont Rivularia, L. pygmaea is also apparently host to a range of other marine and freshwater cyanobacteria, as well as marine eukaryote algae in the family Ulvophyceae (Chlorophyta). We propose that symbiosis with multiple freshwater and marine cyanobacteria and eukaryote photobionts may contribute to the ability of L. pygmaea to survive the harsh fluctuating environmental conditions of the intertidal zone.