Due to the close linking between the biosphere and atmosphere, there are clear impacts of changes in climate, atmospheric deposition of nutrients/pollutants and land use (Global Changes) on the terrestrial biosphere. Lichens, with a direct dependence on atmospheric conditions, are much more affected by their immediate microclimate than by the ecosystem’s prevailing macroclimate. In contrast to higher plants, poikilohydric organisms have different mechanisms of water and CO2 exchange. The application of stable isotopes to the understanding of the mechanisms that are fundamental to lichen gas exchange and water uptake is a promising tool for the evaluation of lichen response to environmental changes. Indeed, lichens have been shown to be influenced by a large number of natural and anthropogenic environmental factors, serving as ecological indicators. Thus, we may use these organisms to model the impact of key global change drivers, such as nitrogen deposition and biodiversity changes, at local scale. Particularly useful is the application of the Lichen Diversity Value (LDV) in order to evaluate the impact of global drivers. Moreover, it has been shown that these indices, associated with main photobiont types, green-algae (LDVch) or cyanobacteria (LDVcyh), and/or nitrophilous versus oligotrophic species, were good candidates as ecological indicators. Besides mapping with high spatial resolution the effects of climate alterations, lichen functional groups could also be used as an early-warning system in order to detect the first effects of climate change in ecosystems before sudden shifts occur on other components that may be less sensitive. Clearly, lichens possess the adequate traits to be used as powerful indicators of complex interactions between atmosphere and biosphere, and thus can generate potentially interesting models for global change drivers.