In the framework of the Dead Sea Deep Drilling Project, a geomicrobiological investigation has taken place to understand the extent and characteristics of life in the hypersaline sediment of the Dead Sea. The DNA recovered in the ICDP cores suggests that different microbial assemblages are associated with particular sedimentary facies, regardless of their depth and in situ salinity. Since this facies are controlled by changes in the evaporation-precipitation ratio in the region, our data suggest that subsurface microbial assemblages are themselves highly influenced by climatic variations at the time of sedimentation. In particular, humid periods allow the development of varied metabolisms such as sulfate reduction, methanogenesis and potentially anaerobic methane oxidation, deeply influencing the carbon and sulfur cycles of the lake, and subsequently allowing the formation of diagenetic Fe-S minerals. These results reveal the importance of considering microbial impact on archives retrieved from lacustrine drilling project, even in extreme environments.