The primary succession of ectomycorrhizal (ECM) fungi has been well described forPinusandSalix, but the succession for other pioneer hosts is almost unknown. Here, we investigated ECM fungal communities ofAlnus sieboldianaat different host growth stages in a primary successional volcanic site on Izu-Oshima Island, Japan. ECM root tips were collected from 120 host individuals, encompassing seedling, sapling, and mature tree stages. The taxonomic identity of the ECM fungi was determined based on rDNA internal transcribed spacer region sequences. Nine molecular taxonomic units were detected from a total of 807 root tips. The initial ECM fungal community on the pioneer seedlings was composed of only three species, where an undescribedAlpovaspecies (Alpovasp.) was exclusively frequent. With host growth, other ECM fungal species were added to the communities, while the initial colonizers remained even at mature tree stages. Thus, the ECM fungal composition significantly changed along host growth stages and showed the nested community structure. Although most of the ECM fungi confirmed in this study had a broad Holarctic geographical distribution, theAlpovasp. had no previous records in other regions. These results suggest that a locally evolvedAlpovasp. plays an essential role in the initial seedling establishment ofA.sieboldianaat early successional volcanic sites.Supplementary InformationThe online version contains supplementary material available at 10.1007/s00572-023-01112-w.