The sexually reproducing lichen-forming fungus Ramalina fraxinea associates with at least seven different Trebouxia lineages.

These lineages belong to at least two species: T. decolorans and T. jamesii, which coexist within each analyzed thallus.

Some of these lineages are shared in different extent by several other lichen taxa.

The different algal lineages observed may be consequence of an incipient speciation within T. decolorans.

This study stresses the importance of coordinated ultrastructural and phylogenomic analyses in phycobiont diversity estimates.