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<i>Rhizopogon</i> (Boletales) is an ectomycorrhizal (ECM) fungal genus that forms specific symbiotic associations with host trees within the family Pinaceae, playing a crucial role in seedling growth and establishment. Despite its ecological importance, the species diversity and phylogenetic relationships of <i>Rhizopogon</i> in East Asia remain poorly understood. Here, we investigate the diversity, phylogeny, and host specificity of Japanese <i>Rhizopogon</i> species. We conducted phylogenetic analyses of 106 basidiomata and three ECM root tip samples collected across Japan using three loci: the internal transcribed spacer (ITS), large subunit ribosomal RNA (LSU), and RNA polymerase II subunit B (<i>RPB2</i>). Phylogenetic analyses revealed at least 16 distinct lineages, including one only detected from a single root tip collected in Japan. Among the lineages with basidiomata, five corresponded to previously described species (<i>R. alpinus, R. boninensis, R. lucidus, R. togasawarius</i>, and <i>R. yakushimensis</i>). Seven other lineages, which did not cluster with any previously recognized species, are described here as new species and detailed morphological characteristics are provided: <i>R. citrinus, R. filivolubilis, R. flavoroseolus, R. japonicus, R. melliodorus, R. margaritaceus</i>, and <i>R. politus</i>. Two other lineages are new to Japan: <i>R. pseudoroseolus</i> and <i>R. evadens</i>. Another lineage, previously regarded as the Japanese "Shouro," was reidentified as <i>R. graveolens</i> based on morphological and molecular evidence. This study is the first comprehensive taxonomic assessment of <i>Rhizopogon</i> in East Asia.