Background: Alpine alder vegetation acts upon the nearby grass and dwarf shrub vegetation by the nitrogen supply from the symbiotic bacteria Frankia alni of Alnus viridis. This has been studied in two transects concerning plant distribution, plant diversity, nitrate concentration in soil and photosynthetic performance of specific marker plants. Results: Away from the alder stand, a band of some meters was dominated by Calamagrostis varia which then was followed by alpine dwarf shrub vegetation. Nitrate in the soil showed a concentration decrease away from the alder stand leading to values near the detection limit in the dwarf shrub zone. Within these three zones, plant species were distributed according to their N-index, given in the ecological literature. Three dominant species, Calamagrostis varia, Rhododendron ferrugineum and Vaccinium myrtillus were examined at sites of different N-availability in the horizontal transect for their photosynthetic performance, by measuring the prompt fluorescence, the OJIP named polyphasic rise of chlorophyll-a fluorescence. All three plant species showed signs of stress in the fluorescence rise kinetics at decreased nitrate availability. These are similar to other known stress effects such as faster reduction of the primary acceptor or an electron supply limitation on the donor site of photosystem II. Conclusion: Prompt chlorophyll-a fluorescence data of the examined leaves in a natural vegetation system showed the effects of a decrease in the essential nutrient nitrogen and in a manner parallel to changes in plant diversity. The selected marker plants behaved differently towards decreasing nitrogen concentrations in soil.