Arbuscular mycorrhizal fungi (AMF) play a significant role for mine tailing rehabilitation due to their sensitivity towards a range of soil pollutants. This beneficial biological agent can enhance plant tolerance to heavy metal contamination. This study screened indigenous AMF associated with growing indigenous ferns and grasses in the mine tailings for potential use in rehabilitating a 3-decade abandoned mined out area in Mogpog, Marinduque. Pterocarpus indicus Willd. (narra) was used as the host plant to establish mycorrhizal fungi association. Among the treatments, indigenous AMF associated with Ferns 1, 2 and 5 generally improved the height and shoot diameter of the narra seedlings and the effect was comparable with commercially available AMF inoculants, MYKOVAM® and MYKORICH®. The dry weight of the roots and nodules was consistently improved by indigenous AMF from Fern2 and Grass1, which had comparable effect with MYKOVAM® and MYKORICH®. Overall, the total seedling dry matter of narra seedlings was significantly stimulated by AMF, irrespective of isolates’ origin. The mycorrhizal root infection by AMF and number of spores in the soil were all high as compared with the uninoculated control counterpart. Lastly, AMF inoculation induced Cu retention in the roots of the seedlings. Thus the results imply that, the mined out indigenous AMF are potential agents to rehabilitate the abandoned mine tailings in the Philippines.