Several modelling species distribution studies have been developed, in last years, though mainly applied in higher plants, mammals or birds. However, little is known about overlooked taxa like lichens. We have evaluated the potential distribution of eleven threatened lichens in Spain and how the Natura 2000 network contributes to protect them. To overcome difficulties related to the lack of systematic surveys in those poorly known species we used only-presence data by means of ENFA (ecological-niche factor analysis). Then, we used ENFA to model the environmental niche of each species and to obtain the habitat suitability maps. In order to test the effectiveness of the Natura 2000 network, the habitat high suitability map for all species was overlapped with the network map. Our results show that all species considered present habitats requirements different from the average conditions of Spain, although clear differences exist among the species. That is, Peltigera elisabethae shows an extremely narrow niche, whereas Peltigera neckeri presents the highest ecological breadth. High temperature and long drought periods are the variables which restrict more the occurrence of these species. So, all species appear mainly confined to well-conserved forest and mountain ranges where these variables are dimmed. This mainly occurs in the oceanic northern fringe and in the higher Mediterranean mountains. In relation to the success of the Natura 2000 network, our results show that the capability of this network to protect key habitats for these species seem to be guarantied, probably because most reserves appear in mountainous areas in Spain. Evaluation of reserve network effectiveness needs the use of this type of gap analysis and especially the inclusion of ‘not charismatic’ organisms such as lichens.