Mining activities are highly polluting and generate significant quantities of wastes that have a deleterious impact on the environment and human health. More specifically, phosphate mining substrates are generally of poor quality to allow the installation and the growth of plants in semi-arid areas, with a destructured soil, very rich in phosphate, and possibly contaminated with metals and metalloids. Microorganisms could strongly accelerate the process of phytostabilisation, like microbial communities play a central role in the functioning of this compartment, ensuring the recycling of organic matter and nutrients. They are also strongly involved in plant growth promotion. Other organisms can also be implicated in the mobilization/immobilization of metals and metalloids in the soil. In our study, microbial communities present in a moroccan phosphate mine wastes were characterized using Illumina MiSeq sequencing. In silico analysis revealed that the majority of sequences belong to Proteobacteria and Bacteroidetes. Among those microorganisms, some have plant growth-promoting traits and can be beneficial for the establishment of a vegetative cover, which can be an effective and economic tool to stabilize the soil and re-entering the site in the surrounding landscape. This finding could be pivotal for the revegetation of phosphate mine wastes, a national priority for Morocco, producing millions of tons of phosphate wastes each year.