Habitat fragmentation is a critical issue for biodiversity conservation, disrupting ecological processes and species interactions. While its effects on many organisms are well studied, impacts on symbiotic systems remain poorly understood. Lichen symbi- oses, in particular, have been widely investigated, but most work has focused on the fungal partner. To our knowledge, this is the first study to assess how forest fragmentation and structure influence photobiont diversity in epiphytic lichen communities. We analysed over 2000 thalli from 44 mycobiont species across 28 genera in a fragmented Mediterranean forest using high- throughput sequencing. We identified 33 algal species across three genera, including two putative undescribed taxa. Several lineages were newly recorded for Europe and the Iberian Peninsula, highlighting that green algal photobiont diversity remains substantially underestimated. Mycobiont identity emerged as the primary driver of photobiont community structure. In addition, forest structure and fragmentation variables were significantly associated with photobiont diversity. However, it remains possible that these effects drive photobiont diversity by directly influencing lichen holobionts. Overall, our results indicate that variation in green algal photobiont diversity is closely linked to the richness of their fungal partners, with any effects of fragmentation likely mediated through changes in mycobiont communities. Keywords: community structure | habitat fragmentation | high-throughput sequencing | lichen symbiosis | Mediterranean forest | photobiont diversity | Trebouxia.