Cyanobacteria and eukaryotic algae were investigated during three seasons in 18 plots established across Sverdrup Pass valley of central Ellesmere Island, 79°N, Canada. The sites differed in altitude, substratum, and other characteristics. A high species diversity totalled 136 taxa. Cyanobacteria accounted for 52 and eukaryotic algae 84 species. In both groups, numerous species did not correspond to any taxa described. However, high diversity did not always coincide with high algal abundance or biomass. On older and stable landscapes, visible crusts developed, containing mostly cyanobacteria, fungi, and other microbial components. Considerable variation in algal diversity and abundance was found among the sites. Also the southern, granitic portion of the pass was richer in green algae compared to its northern, dolomitic portion where motile cyanobacteria were more prominent. These micro-autotrophs occupied the soil profile to a depth of 7 cm. Their highest density was not at the surface but at 3–4 cm depth. One plot was contaminated by windblown copper-rich dust from a nearby outcrop and soil here was poorest in content of photosynthetic pigments, suggesting a local heavy-metal toxicity.