Biological soil crusts (BSCs) fulfil numerous ecological functions in arid and semiarid areas. Cyanobacteria are important BSC organisms, which are responsible for carbon fixation, N2 fixation and binding of soil via extracellular polysaccharides. The cyanobacterial populations were characterised in different sampling plots established in three experimental stations along a rainfall gradient within NW Negev Desert, Israel. Cyanobacterial crust thickness and osmolyte accumulation therein decreased in plots with lower moisture. The cyanobacterial population structure also changed in different plots. We observed an increase of subsection III cyanobacteria such as Microcoleus spp. and Leptolyngbya spp. and a decreasing proportion of strains belonging to subsections I and IV in drier areas on the rainfall gradient. This population shift was also observed in the sampling plots, which were situated at various relief positions within the sand dune experimental sites. We also characterised the cyanobacterial populations within mechanically disturbed plots. After 4 years, they reached between 80% and 50% of the control populations in the northernmost and southern stations, respectively. Our results suggest that the cyanobacterial population is sensitive not only to macroscale factors but may also be subject to local climate variations and that 4 years was insufficient for complete recovery of the cyanobacterial population.