The most important hypersaline environment in Bolivia is the Uyuni salt flat. It is the largest salt flat in the world and, it presents certain unique chemical characteristics and composition on its surface such as a gradient of ion concentrations from south to north. The autochthonous microbial communities in these salt flats have yet to be studied in detail, and it is not clear if these communities are somehow homogeneous across in the ca. 10,000 km² flat. The present study was done in order to describe the structure of the microbial communities and determine any possible correlations with abiotic factors. Total DNA was extracted from rock salt samples obtained at different locations, and 16S rDNA followed by Terminal Restriction Fragment Length Polymorphism (T-RFLP) analyses. Statistical analyses of the communities indicated that the highest diversity indices were found in the southern area, and the microbial communities were clustered in three groups for bacteria and in two groups for archaea. This variation could be explained by different concentrations of lithium and calcium, in addition to other abiotic variables on the surface crust. Our results indicate that even under extreme hypersaline conditions abiotic factors such as wind or geological activity may determine the composition of the resident microbiota.