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The cyanobacterial layer (1-3 mm) of microbial mats of Wadi Muqshin, Sultanate of Oman, in hypersaline continental pools near the Empty Quarter desert were analyzed for cyanobacterial diversity, pigments composition and antibacterial and quorum sensing inhibition activities at the microbial community level. The salinity of the ponds reached up to 75 parts per thousand, the temperature was around 49 degrees C and the salt composition was similar to seawater. Cyanobacteria in pools containing coccoid and filamentous forms similar to those normally found in salt ponds and in intertidal flats were found. Among the observed taxa were Microcoleus chthonoplastes, Spirulina subsalsa, Johannesbaptistia pellucida, Chroococcidiopsis sp., Aphanocapsa sp., Chroococcus sp., Gloeocapsa sp., Schizothrix sp. and Leptolyngbya sp. Using high performance liquid chromatography (H PLC), the pigments chlorophyll a, scytonemin, chlorophyllid a, beta-carotene and fucoxanthin were detected, with the highest concentrations obtained for the ultra-violet (UV) sunscreen pigment scytonemin. The chemical extracts of the microorganisms in the mats cyanobacterial layer exhibited antibacterial activity against 3 out of 9 tested pathogenic bacterial strains and showed quorum sensing inhibition activity against the reporters Agrobacterium tumefaciens NTL4 (pZLR4) and Salmonella enterica S235 but not Chromobacterium violaceum CV017. We conclude that the studied inland hypersaline microbial mats harbor similar diversity to their counterparts in intertidal flats and evaporation ponds and could produce chemical compounds that are of biotechnological significance.