Freshwater habitats of the Italian Alps are largely unexplored and further floristic-ecological surveys are needed to clarify the role of freshwater lichens in these environments. This applies especially to springs, since they seem to be suitable for a relatively high number of aquatic species due to their ecological stability. The present work is focused on springs in an alpine region, and is centered on: (a) floristics of freshwater lichens of the Italian Alps, (b) ecological and morphological information on potential indicator species for calcareous and siliceous springs. The study was carried out in the eastern Italian Alps on 36 perennial springs. Single springs proved to host a surprisingly low number of species, while at regional level the entire pool of investigated springs host a relevant lichen flora representing 45% of the freshwater lichens of the Italian Alps. One species is new to Italy and 3 are new to Trentino-Alto Adige. Biodiversity conservation measures should therefore be planned at regional level, including a whole network of sites in different altitudinal belts and with different substrates. Verrucaria elaeomelaena and V. funckii are the most frequent species on calcareous and siliceous springs respectively. They are suggested as potential indicator species, since they proved to be indicative of the main physical, ecological and hydrochemical features of their habitat. A detailed morphological description of these two species is also provided in order to enhance their identification by environmentalists.