In mountain desert ecosystems, wetlands around saline and freshwater lakes allow various organisms to thrive and sometimes serve as the only source of drinking water for wild and domestic animals. We present results concerning diversity and structure of cyanobacterial inoculum from Eastern Pamir Mountains' benthic sediments, collected from small water bodies with contrasting salinity, temperature and other chemical parameters. We used morphological identification and molecular NGS techniques based on the amplification of the V3-V4 hypervariable region of 16S rRNA gene. Only a few cyanobacterial taxa have been identified in the preserved samples, while 27 taxa were successfully isolated and identified from the benthic sediments. Metagenomic analysis revealed that the cyanobacterial contribution to benthic bacterial communities was low. Representatives of the order Nostocales dominated in the samples, followed by Synechococcales, while contributions of Oscillatoriales and Chroococcales was much lower. The correlation matrix for the amplicon-based composition of samples clustered together samples of similar salinity and temperature. However, in hierarchical clustering of taxonomic structure of samples, communities with similar structures were not grouped by salinity or temperature. These results suggest that salinity and to some extent temperature, influence the composition of the inoculum, although the structure of the cyanobacterial communities is further shaped by other factors. Our study also demonstrated that the benthic inoculum for cyanobacterial communities contained potentially toxic taxa characteristic of both benthic and planktonic communities.