Cyanobacteria are primary colonizer and dominant component of soil photosynthetic communities in BSCs.They are crucial in improving soil environments,namely accumulating soil C and N.However,research on species composition of microorganism and ecological function mainly focuses on bacteria and relatively few studies on cyanobacteria were conducted.We employed 454 pyrosequencing of 16S ribosomal RNA to investigate the composition and distribution of cyanobacteria on regional scales in the Gurbantunggut Desert.The relationship between cyanobacterial distribution and its environmental factors were also explored.A total of 14384 cyanobacteria 16S rRNA gene,partial sequences was obtained.507 OTUs with the most reads were selected due to that most OTUs had very few reads.Among them,334 OTUs sequences were of cyanobacteria origin,belonging to Oscillatoriales,Nostocales,Chroococcales and uncultured cyanobacterium clone.Microcoleus vaginatus,Chroococcidiopsis sp.were dominant species and main contributor in the accumulation of organic C in most areas of the Gurbantunggut Desert.Except that,M.steenstrupii,other Microcoleus species,Scytonema sp.,Nostoc sp.,and Oscillatoria amoena were common species.Species composition and abundance of cyanobacteria also showed distinct variations.Soil texture,precipitation,nutrients and salt had effects on cyanobacterial distribution.Increased precipitation was helpful to improve cyanobacterial richness and algal biomass.Higher content of coarse sand promoted the colonization and growth of Osillatoriales(mainly Microcoleus spp.)and Chroococcales(mainly Chroococcidiopsis spp.).The fine-textured soil with higher nutrients and salt supported more varied populations of cyanobacteria,namely some heterocystous cyanobacteria(Nostoc sp.and Scytonema sp.).The results suggested that cyanobacteria had high richness in the Gurbantunggut Desert and precipitation was a primary regulating factor in cyanobacteria composition in regional scale.