For greening at mine sites, plant species that accumulate metals in tissues and are tolerant to high metal concentrations should be selected from the perspective of phytostabilization. Artemisia indica var. maximowiczii is a commonly used plant for greening in Japan and several studies have shown that A. indica var. maximowiczii grown on metal-concentrated soil accumulated high concentrations of metals in tissues. Additionally, recent studies suggested that root endophytic fungi can enhance metal tolerance for host plant. The purpose of our study is to elucidate the metal tolerance mechanism of A. indica var. maximowiczii grown naturally at mine site, considering the effects of root endophytic fungi. The elemental concentrations of A. indica var. maximowiczii collected from a mine site were analyzed by ICP-OES and the plant highly accumulated Fe, Al, and Cu in roots, indicating metal tolerance. HPLC-DAD and LC/MS analysis showed that chlorogenic acid and 3,5-dicaffeoylquinic acid were detected as metal detoxicants in roots. Several root endophytes were isolated from A. indica var. maximowiczii roots; isolated fungi will be tested by CAS assay to confirm siderophore production abilities, which would enhance functional effects on metal tolerance of host plant. It is necessary to clarify the plant-fungi interaction via inoculation test.