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Toxic metabolites are produced by many cyanobacterial species. There are limited data on toxigenic benthic, mat-forming cyanobacteria, and information on toxic cyanobacteria from Central Asia is even more scarce. In the present study, we examined cyanobacterial diversity and community structure, the presence of genes involved in toxin production and the occurrence of cyanotoxins in cyanobacterial mats from small water bodies in a cold high-mountain desert of Eastern Pamir. Diversity was explored using amplicon-based sequencing targeting the V3-V4 region of the 16S rRNA gene, toxin potential using PCR-based methods (<i>mcy, nda, ana, sxt</i>), and toxins by enzyme-linked immunosorbent assays (ELISAs) and liquid chromatography-tandem mass spectrometry (LC-MS/MS). Molecular identification of cyanobacteria showed a high similarity of abundant taxa to <i>Nostoc</i> PCC-73102, <i>Nostoc</i> PCC-7524, <i>Nodularia</i> PCC<i>-</i>935 and <i>Leptolyngbya</i> CYN68. The PCRs revealed the presence of <i>mcyE</i> and/or <i>ndaF</i> genes in 11 samples and <i>mcyD</i> in six. The partial sequences of the <i>mcyE</i> gene showed high sequence similarity to <i>Nostoc</i>, <i>Planktothrix</i> and uncultured cyanobacteria. LC-MS/MS analysis identified six microcystin congeners in two samples and unknown peptides in one. These results suggest that, in this extreme environment, cyanobacteria do not commonly produce microcystins, anatoxins and cylindrospermopsins, despite the high diversity and widespread occurrence of potentially toxic taxa.