Abstract:Aims It is well known that desert algae play significant and irreplaceable roles in the early formation and structural maintenance of the biological soil crusts. Although species composition and community structure of algae have be en widely studied, only a few investigations have been made on the vertical distribution of soil algae in deserts. Our objective was to further reveal species community structure and ecological distribution of desert algae in vertical layers. Methods We selected typical sand dunes in the Third Site of the southern Gurbantunggut Desert and collected 112 soil samples twice in summers of 2005 and 2006. Using a fixed section from different locations of the sand dunes, we gathered soil samples at serial sections of 0-0.5，0.5-1，1-2, 2-5 cm depth respectively. Algae species were identified by direct microscopic observation and liquid culture observation (dominant species were identified by direct observation). Each sample was checked three times, with ten observations for each sample. Algae biomass was determined by measurement of chlorophyll a. Important findings Algae species composition differ among soil layers. Dominant algae species are mainly in the 0-2 cm layers and seldom exist in lower layers. The most dominant algae species in most layers is Microcoleus vaginatus.In 1-2 c m layers of interdune and windward, Oscillatoria pseudogeminata is the most dominant. In addition, Synechocystis crassa, Naviculasp. and Amphora ovalis are more dominant than other algae. Except for the top of sand dunes, algae biomass in different layers exhibited highly significant differences (p<0.01) at other locations. Algal biomass dramatically decreased with soil depth from the surface to lower levels. At the same soil depths, algae biomass declined from the inter dune position to the windward and leeward, to the top, with differences highly significant (p<0.01) or significant (p<0.05).