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Algal-cyanobacterial component of 51 soil samples collected from 27 locations, representing varied agroecological regions of Thar desert of India was analysed using enrichment culture technique in presence and absence of nitrate nitrogen fortification of BG 11 medium. The soils were alkaline, poor in nutrients and showed large variations in conductivity and water soluble cations Na+, K+ and Ca2+). The samples harboured 79 morphotypes belonging to 21 genera of cyanobacteria and four morphotypes belonging to three genera of green algae. The unbranched cyanobacteria dominated the flora. Phormidium > Oscillatoria > Lyngbya exhibited maximum morphotypic diversity on N supplementation while Anabaena was the most diverse genus followed by Nostoc, Scytonema and Calothrix in the absence of N supplementation. Morphotype richness varied from 1 to 6 and the frequency was < 18% for non-diazotrophs and < 51% for diazotrophs. Non-repeatability of forms was as high as 66%. Shannon and Weaver’s diversity index was very low for both +N and -N enrichments. Principle component analysis suggested that variation in chemical composition of the soil did not influence the algal-cyanobacterial diversity. The structure of community composition was found to be more homogeneous in non-sandy, crusted and vegetated soils than in sandy, non-crusted and barren soils, suggesting that the incidence and colonisation of desert soils by cyanobacteria is predominantly a function of agroecological conditions. On the contrary, vegetated and non-sandy soils showed presence of large number of infrequent morphotypes. (C) 2007 Elsevier Ltd. All rights reserved.