The availability of highly variable markers for the partners of a fungal symbiosis enables
the integrated investigation of ecological and evolutionary processes at the symbiotic level.
In this article we analyze the specificity of the first and to date only microsatellite markers
that had been developed for an epiphytic lichen (Lobaria pulmonaria). We used DNA extracts
from cultures of the fungal and of the green algal symbionts of L. pulmonaria as well as total
DNA extracts from related Lobaria species associated with the same algal partner, and got
evidence that five of the previously described microsatellite markers, proposed to be fungus-specific,
are indeed alga-specific. Hence, highly variable microsatellite primer sets
available for both, the algal and the fungal symbionts of L. pulmonaria are now at our hands,
which allow us to investigate so far unexplored biological processes of lichen symbionts,
such as codispersal and coevolution. In a broader sense, our work evaluates and discusses
the challenges in developing biont-specific molecular markers for fungi forming close associations
with other organisms.