Range‐wide sampling reveals cryptic lineages but largely conserved mycorrhizal associations in the Japanese fairy lantern Thismia kobensis

Societal Impact Statement The jewel‐like flowers of Thismia are as rare as they are beautiful, often recorded from only a single site per species. Access to 15 populations of T. kobensis has enabled an uncommon, range‐wide assessment of morphology, genetics, and fungal partners. Our analyses showed that T. kobensis comprises three cryptic lineages that rarely exchange genes, despite their nearly identical flowers. Across most of its range, two lineages consistently associate with the same fungal lineage, whereas a small northern lineage depends on different fungi. These findings highlight the need to conserve each lineage separately, with special attention to the vulnerable northern group. Summary Thismia (Thismiaceae) includes some of the most elusive angiosperms, with many restricted to their type localities. Limited dispersal may foster cryptic diversity within isolated populations, complicating species delimitation. Although many Thismia species display high mycorrhizal specificity, whether such specificity is consistent within species remains unclear due to the paucity of comparative population‐level studies. Thismia kobensis , with 15 extant populations, offers a valuable model for investigating population structure and mycorrhizal associations. We examined inner floral morphology and genome‐wide SNPs to evaluate morphological and genetic differentiation across all known T. kobensis populations. Population genetic analyses, including Mantel tests, were conducted to identify factors that shape genetic structure, and fungal barcoding was used to assess associations between plant genotypes and fungal partners. MIG‐seq data identified three genetic groups with minimal gene flow, despite the largely uniform floral morphology. One group was widespread, whereas the other two were confined to the northern Kinki region. Mantel tests detected no significant isolation‐by‐distance patterns, suggesting restricted dispersal even across short distances. Genetic structure showed limited correspondence with mycorrhizal associations: VTX00113 predominated overall, while the rarest group primarily associated with VTX00106 and VTX00295. These findings suggest that T. kobensis may comprise multiple cryptic species or distinct evolutionary lineages. The presence of VTX00113 in two genetic groups indicates a conserved fungal association, whereas the distinct partners in the rarest group may reflect genetic divergence mediated by host shifts. Additional data on fungal communities in surrounding soils and autotrophic plants are needed to clarify partner selectivity among groups.