Ultramafic substrates impose severe edaphic stress characterised by metal toxicity, nutrient imbalance, and extreme microclimatic conditions, creating spatially fragmented habitats that can shape evolutionary and ecological dynamics of associated organisms. Together with climatic variation, such factors may also influence the structure of holobiont communities of lichenized fungi. Here we investigated the ultramafic specialist lichen Solenopsora liparina across its entire range. We contextualized its symbiotic associations using calcicolous congeners (S. candicans and S. cesatii), as ecological reference taxa representing contrasting substrate-associated lineages within the sampled dataset, to assess how climatic filtering acting within a specialised edaphic niche structures symbiotic partner diversity and composition. Photobionts and endolichenic fungi displayed climate-associated compositional turnover and lineage-level diversity. Variation in the composition of these symbionts was most strongly associated with precipitation during the warmest quarter and, in photobionts, with altitude and temperature seasonality. In photobionts, dominant lineages differed in their relative occurrence among host taxa, whereas low-abundance lineages were broadly shared across samples within the dataset. Despite this turnover, alpha diversity remained generally stable across environmental gradients, indicating that climatic variation most strongly affects community composition rather than within-sample diversity. The results are consistent with a model of mixed host- and substrate- associated symbiont assembly, in which dominant photobiont lineages exhibit host- or substrate-linked preferences, whereas low-abundance associates show weaker specificity and broader ecological overlap across environmental and host contexts. Overall, the findings indicate that climatic factors structure the composition of symbiotic partners without strongly altering their overall diversity, while variation among host taxa is reflected in lineage turnover of dominant symbionts. The persistence of the ultramafic specialist lichen S. liparina thus appears to rely on flexible, compositionally dynamic symbiotic associations shaped by climatic variation within a spatially and edaphically constrained niche, rather than obligate partner specificity. Substrate effects are interpreted here as host-associated lineage patterns rather than independently quantified drivers. More broadly, the results suggest that climatic variation can in some cases strongly influence symbiotic assembly within environmentally extreme and spatially heterogeneous systems. Substrate specialisation provides the ecological context in which such interactions occur. Together, the findings highlight the importance of climatic variation in shaping symbiotic assembly within an edaphically specialised system, emphasizing that patterns associated with host and substrate context are expressed mainly through lineage turnover rather than wholesale community replacement. Key words: Endolichenic fungi, holobiont, lichen, metabarcoding, Symbiochloris, ultramafites.