Arbuscular Mycorrhizal Fungi (AMF) form symbiotic associations with the roots of many plants, and contribute to soil aggregation, structural stability and yield of plants in soils with low fertility. They have also been associated with cleaning of metal polluted soil. This study investigates the potential of AMF indigenous (Scutellospora reticulata and Glomus pansihalos) to Southern Guinea Savanna ecological zone of Nigeria to enhance phytoremediation of soils contaminated with Aluminium (Al) and Manganese (Mn). A 4x3x2 factorial pot experiment was used to assess the phytoremediation potential of indigenous AMF of alfisols contaminated with Al and Mn cropped with cowpea. The concentrations of the metals in soils and plants were determined by atomic absorption spectrophotometer. Data were analysed using Analysis of Variance (ANOVA). Both S. reticulata and G. pansihalos significantly reduced Al (F5, 21=791.4; p< 0.05) and Mn (F5, 21 =286; p< 0.05) contents of soils polluted with these metals. S. reticulata however showed a significantly higher remediating ability than G. pansihalos. It was observed that soil properties had a significant impact on bioremediation by AM fungi. It was concluded that S. reticulata and G. pansihalos indigenous to southern Guinea savannah have the potential for use in phytoremediation of soils polluted with Aluminium and Manganese.