In this study, biological soil crust and cyanobacterial hypersaline mats from the Sultanate of Oman were microbiologically investigated. Different biological soil crusts (SD, GY, WK and AD) from different geographical locations were compared for their characteristics, cyanobacterial diversity, chlorophyll a content and nitrogen fixation rates using acetylene reduction assay. The cyanobacterial diversity was studied using direct microscopy, enrichment cultivation and molecular tools. The response of cyanobacteria to wetting and desiccation was checked at different conditions. The cyanobacteria that exhibited hydrotaxis were identified by direct picking up and sequencing of their filaments. The diversity of cyanobacteria and halophilic archaea from Maqshan hypersaline mats was also investigated. The potential of both ecosystems to produce antibacterial compounds as well as antifouling compounds was tested using disc diffusion bioassays and quorum sensing inhibition procedure. The cyanobacterial composition of all biological soil crusts was very similar with little variation despite their geographical locations and soil structure. This was supported through direct microscopy and isolation. Filamentous and unicellular cyanobacteria were işolated including Microcoleus vaginatus, Scytonema, Leptolyngbya, Lyngbya, Nostoc, Xenococcus and Chroococcus. All isolates were capable of fixing nitrogen. Nitrogen fixation rates of all crust samples were comparable in the dark and light. The greening of biological soil crust shortly after water addition was found to be due to migration coupled with an increase of chloroplast content per cell. The dramatic increase in chlorophyll a after 24 hours suggests the trapping of filaments at the surface as well as microbial proliferation. The migrating filamentous cyanobacterium in all crust samples was Microcoleus. The fatty acid analysis of these crust samples before and after wetting revealed similar fatty acid compositions indicating that the microbial composition is more or less stable. The cyanobacterial hypersaline mats from Maqshan revealed the presence of a number of filamentous cyanobacteria including Microcoleus Chthonoplastes, Leptolyngbya, Phormidium, Spirulina and Plectonema and unicellular cyanobacteria belonging to Xenococcus, Aphanothece, Cyanothece, and Chroococcus genera. Haloterrigena thermotolerans (SK5) and H. saccharevitans (SK6) Archaea were isolated along with others (SK2, SK3 and SK4). The isolates grew optimally above seawater salinity and between 20-40°C but SK6 that could grow optimally between up to 30-50°C. The strains are, thus halophilic and mesophilic in nature except for the SK6 isolate which is moderately thermotolarent. Biological soil crust and hypersaline mats extract had some QSI activity against Agrobacterium tumefaciens and Salmonella S235 along with some antibacterial activity against Streptococcus pyogenes, Staphylococcus aureus and Pseudomonas aeruginosa.