Abstract: Twenty-two species of algae, including 10 Cyanophyta,4 Chlorophyta,6 Bacillariophyta and 2 Euglenophyta,were isolated and identified from the semi-desert algal crusts in Shapotou,Ningxia Autonomous Region.The relationship between algae and soil matrix was studied by grinding and superprobe,and the distribution of algal species in eight layers of crusts was examined under light and scanning electron microscopes.It was found that the algae exhibited a layer typed distribution in intermicron, and the layers of algal crust from surface to inner were in order of inorganic mineral protection layer(ca.0.02mm),alga enriched layer(0.02～2.5mm)and sparse algae layer(2.5～5.0mm).The filaments of algae were united with clay mineral by the polysaccharides and protein of their sheath,or extended directly into mineral granules to network and band sand and soil particles.