Waste dumps generated by mining activities contain heavy metals that are dispersed into areas leading to significant environmental contamination. The objectives of this study were (i) to survey native plants and their associated AM fungal communities from waste soils in a Moroccan mine site and (ii) to follow Eucalyptus growth in soil collected from the waste-mine. AM spores from native plant species were collected from the mining site and the surrounding uncontaminated areas were multiplied and inoculated onto Eucalyptus camaldulensis. The results showed that (i) the native plant species recorded in the waste did not show an active metal uptake, (ii) the selected native plant species are associated with AM mycorrhizal fungi and (iii) the use of AM fungi adapted to these drastic conditions can improve the growth of the fast-growing tree, E. camaldulensis and its tolerance to high soil Cu content. In conclusion, it is suggested that in order to define efficient low-cost phytostabilization processes, the use of native resources (i.e., mixtures of native mycorrhizal fungi) in combination with fast-growing tree species such as Eucalyptus, could be used to optimize the establishment of a permanent cover plant in contaminated areas.