Across much of lowland Britain, lichen diversity has been dramatically affected by the Industrial Revolution, including the lasting legacy of pollution, and changes in land use including the loss, intensification, or abandonment of traditional woodland management. We sampled preserved epiphytes on historical timbers in vernacular buildings to reconstruct pre-industrial lichen species occurrence for a site in Exmoor, south-west England, and used these data to quantify biodiversity loss that appears related to shifts in woodland composition. A total of 33 lichen epiphyte species were collected from pre-industrial structural timbers, and these were compared with modern lichen occurrence. Based on a direct comparison with species presence-absence in the same 10 km target grid-square, c. 31% of species recorded from the pre-industrial landscape had disappeared from the post-1960 landscape. Based on statistical inference comparing historical records with present-day biogeographical distributions, up to 38% of species could be inferred to be lost. This study presents a surprisingly high figure for these losses for a region in Britain usually recognized as having a relatively unpolluted environment and a diverse set of lichens. Of 12 species that were inferred to be lost, nine are predominantly found on nutrient-rich bark, and in our study on Ulmus, the dominant timber in the archaeological samples. We conclude that shifts in phorophyte distribution and abundance may be more important in this region than previously understood.