Five different soil rhizosphere samples were collected from the following medicinal plants: Heliotropium pterocarpum, Euphorbia cuneata, Dracaena ombet, Balanites aegyptiaca and Prosopis juliflra located in HalayebShalateen region, Egypt. Physico-chemical characterization of these soil was performed. Also, six microbial DNA extraction protocols (A-F) including hexadecylmethylammonium bromide (CTAB) and sodium docdeylsulfate (SDS)- based methods were compared for these soil. Moreover, Phospholipid Fatty Acid (PLFA) analysis was applied to characterize the microbial community structure of these samples. Consequently, this work provides rapid microbial DNA extraction and precipitation method and biodiversity evaluation of microbial community structure in the samples.