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Despite hostile climate in the Kuwait desert, perennial vegetation patches persist but are affected by anthropogenic pressures and need to be conserved or restored to their original state. Our goal was to assess the bacterial community composition and structure in both rhizospheric and bulk (non-rhizospheric) soil samples from protected and unprotected sites of four dominant terrestrial vegetation types in the Kuwaiti desert. The bacterial composition and structure was investigated by Illumina MiSeq sequencing of the 16S rRNA gene. Compared to other desert soils, a relatively high diversity of bacteria was detected in this study. Bacterial sequences were affiliated with 13 phyla, most abundant of which revealed were Actinobacteria, Proteobacteria, Planctomycetes, Acidobacteria, Bacteroidetes and Firmicutes. The bacterial structure also commonly identified as Chloroflexi, Gemmatimonadetes, Saccharibacteria …