<p>Mycoheterotrophic plants, which depend entirely on mycorrhizal fungi for carbon acquisition, often exhibit high specificity toward their fungal partners. Members of Thismiaceae are generally recognized for their extreme mycorrhizal specialization and rarity. In this study, we examined the mycorrhizal associations of <i>Relictithismia</i>, a recently discovered monotypic genus within Thismiaceae, and <i>Thismia abei</i>, a <i>Thismia</i> species with a similar distribution in southern Japan, by employing high‐throughput DNA sequencing of the 18S rRNA gene. Our analyses revealed that both <i>R. kimotsukiensis</i> and <i>T. abei</i> are predominantly associated with two specific virtual taxa (VTX00295 and VTX00106) of the genus <i>Rhizophagus</i> (Glomeraceae). These shared associations may reflect either phylogenetic niche conservatism, in which the common ancestor of <i>R. kimotsukiensis</i> and <i>T. abei</i> retained the same AM fungal partners, or convergent evolution, in which the AM fungal phylotypes were independently recruited due to their potential benefits for these mycoheterotrophic plants. Furthermore, BLAST searches demonstrated that VTX00295 and VTX00106 are widely distributed globally, suggesting that highly specialized mycorrhizal interactions are unlikely to be the primary drivers of the limited distribution and rarity of <i>R. kimotsukiensis</i> and <i>T. abei</i>. Overall, our findings enhance our understanding of high mycorrhizal specificity in Thismiaceae. However, broader investigations, combining extensive sampling of Thismiaceae species with ancestral state reconstruction, are needed to determine whether the shared associations detected here reflect phylogenetic niche conservatism or convergent evolution.</p>