In this study, we examine the potentialities of carbon isotope discrimination, chlorophyll fluorescence and quantitative structure techniques for the evaluation of gas diffusion resistances in lichens. For that, a comparative analysis was performed between two species of Lobaria, one with a cyanobiont exhibiting CO: concentrating mechanism (CCM) activity (L. scrobiculata) and the other with a phycobiont lacking CCM activity (L. pulmonaria). Carbon isotope discrimination (A) was affected by the CCM activity and by the resistance to CO: diffusion to the carboxylation sites. The activity of a C02 concentrating mechanism (CCM), which increases the C02 concentration at the carboxylation site, allowed L. scrobiculata to reach higher photosynthetic rates than L. pulmonaria at high water contents, when gas diffusion limitations are maximal. Margins of the thallus exhibited higher values of A than the central parts in L. pulmonaria but not in L. scrobiculata. The spatial variation of A across the thallus was related to intrathalline differences in the resistance to C02 diffusion, whereas the lack of intrathalline variation of A in L. scrobiculata was interpreted as a consequence of the CCM activity. These results were confirmed by the evaluation of C02 resistances in marginal and central parts of the thallus in both species by means of a new method using chlorophyll fluorescence analysis. The quantitative study of thallus structure of both species also revealed significant differences between the two lichen species. Lobaria scrobiculata exhibited a rather unusual intrathalline structural pattern (e.g. larger thallus density’ in the margins than in the centre of the thallus), which allowed for larger water storage capacities in the most actively growing regions. We suggest that lichens lacking CCM, such as in L. pulmonaria, must enhance gas diffusion by reducing water storage to some extent. Structural and physiological intrathalline differentiation, w ith central parts enhancing water storage and margins enhancing gas diffusion and photosynthesis, seems to be an adaptive compromise of these two opposing problems