To investigate the seedling growth of a biologically invasive larch Larix kaempferi (Lamb.) Carr. on Mount Koma, Japan, seedlings were excavated from three microhabitats (bareground = BA, Salix reinii patch = SP, and Larix understory = LU) in three elevational zones. Seedlings showed the highest ectomycorrhizal (ECM) colonization percentage in the most shaded microhabitat, LU. ECM colonization percentages in BA and SP were found to decrease with decreasing elevation. These results inferred that the ECM colonization percentages were related to seedling growth, particularly in BA and SP. However, the annual seedling growth was not synchronized with the increases in either elevational gradients. Although ECM colonization was most evident in LU, the seedling growth was the lowest. We concluded that the effects of ECM colonization on seedling growth were reduced mostly by microhabitat characteristics.