Using a polyphasic approach, the algal and cyanobacterial diversity in biological soil crusts (biocrusts) from two representative but environmentally differing Arctic moisture gradients (Knudsenheia (KH) and Ossian-Sarsfjellet (OS), Kongsfjorden, NyÅlesund, Svalbard) were studied. In total, 65 species (Cyanobacteria 24, Chlorophyta 23, Charophyta 3 and Heterokontophyta 16) were recorded. Both unicellular and colonial Chroococcus-like and thin-filamentous Leptolyngbya-like cyanobacteria were frequently observed in the studied biocrusts. Green unicellular, packet-like and filamentous Trebouxiophyceae were also very common, whereas Chlorophyceae (mainly Coelastrella-like algae), Ulvophyceae and charophytes occurred only in low numbers. Heterokontophyta were characterized by quite high species diversity and frequency especially Eustigmatophyceae. Where necessary, species were identified based on their SSU rRNA gene and ITS phylogeny. The biocrusts also harboured rare and ecologically interesting genera including Drouetiella, Coelastrella, Watanabea, Streptofilum and Monodopsis, some of which are typical of terrestrial habitats of cold and polar regions. Biocrusts from KH (colder and wetter microclimate) exhibited a higher diversity of algae (49 species) than OS (milder and drier microclimate) biocrusts (39 species), with only 22 species shared by both sites. Decreasing soil moisture concided with a decline in the species number. The diversity of unicellular and colonial cyanobacteria as well as yellow-green algae was significantly reduced, while Ulvophyceae and Charophyta disappeared. Comparison of the species composition of biocrust algae and cyanobacteria in all studied biocrusts showed that algal species mostly grouped by territorial affiliation. HIGHLIGHTS ● 24 species of cyanobacteria, 41 species of algae were found in Arctic biocrusts. ● The identification of 19 species was refined based on SSU rRNA gene and ITS phylogeny. ● Decrease in soil moisture coincided with a decline in the species composition. Keywords: Algae arctic; biocrusts; biodiversity; cyanobacteria; ITS; moisture; Ny-Ålesund; phylogeny; SSU rRNA gene; Svalbard.