The term soil health is employed to describe a soil’s capability to sustain plant diversity similar to that observed in reference plant communities.  Various aspects of the biodiversity of soil micro-organisms are increasingly invoked as indicators of soil health. The description and use of such indicators is continuously altered as microbiology techniques advance. Both functional and phylogenetic aspects of soil microbial communities have been considered. Implementation of such indicators in arid lands is challenged by conditions of minimal carbon and water content, low nutrient availability and extremely variable microbial activity status along seasonal gradients. We explored the relationship between the functional and phylogenetic diversities of soil microbial communities in arid land soils. To allow for extensive variations in soil conditions we compared distinct geographical locations in New Mexico (Chihuahua Desert, and the Arizona/NewMexico Tablelands Plateau) and in north-western Jordan (Al- Badia region), for undisturbed, grazed or remediated surface coal mining sites. At each site we tested surface and subsurface soil samples, including the rhizosphere soils associated with dominant plant species. Functional profiling was carried out via MicroResp™,employing 15 different single carbon source substrates. Microbial phylogenetic diversity was estimated by 454 pyrosequencing of endoITS amplicons, for fungal diversity, and 16s rDNA, for bacterial diversity.  The ability of these measurements to distinguish among the tested soil conditions was verified by employing multivariate, exploratory analyses, followed by multiple regression evaluation of the statistically relevant interactions. This allowed integrative evaluation of genetic and functional profile datasets in the context of the measured abiotic parameters.