As prominent examples for symbiotic interactions, the major part of lichens is built up by two different organisms, a photosynthetically active alga (photobiont) and a heterotrophic fungus (mycobiont). Given the hydrophobic coating of lichen symbionts in the lichen thallus by hydrophobins, the area of direct cell cell contact is of prime importance for the transfer of nutrients and signalling compounds between the symbionts. Genomic analyses reported cell wall remodelling during symbiont interaction. However, no detailed investigation of lichen symbiont interaction zone is available so far. Using Energy-dispersive X-ray spectroscopy (EDS), we show that elemental composition of both symbiont cell walls differs when in contact to the symbiont as opposed to those cell wall areas without contact. Both, nitrogen and sulfur content of cell walls, differ significantly in areas of symbiont cell contacts as compared to non-contact zones. NanoCT imaging revealed that about one fourth of the photosymbiont cell wall is in contact to mycobiont hyphae, and fungal cells have a significantly increased volume if in contact to photobiont cells. We provide a sub µm 3D model of the lichen Xanthoria parietina using nanoCT imaging to foster understanding of the symbiont interaction zone.