Disruptive selection on habitat or host-specificity has contributed to the diversification of several animal groups, especially plant-feeding insects. Photosynthetic plants typically associate with a broad range of mycorrhizal fungi, while non-photosynthetic plants that capture energy from mycorrhizal fungi ('mycoheterotrophs') are often specialized towards particular taxa. Sister myco-heterotroph species are often specialized towards different fungal taxa, suggesting rapid evolutionary shifts in specificity. Within-species variation in specificity has not been explored. Here, we tested whether genetic variation for mycorrhizal specificity occurs within the myco-heterotrophic orchid Corallorhiza maculata. Variation across three single-nucleotide polymorphisms revealed six multilocus genotypes across 122 orchids from 30 sites. These orchids were associated with 22 different fungal species distributed across the Russulaceae (ectomycorrhizal basidiomycetes) according to internal-transcribed-spacer sequence analysis. The fungi associated with four out of the six orchid genotypes fell predominantly within distinct subclades of the Russulaceae. This result was supported by Monte Carlo simulation and analyses of molecular variance of fungal sequence diversity. Different orchid genotypes were often found growing in close proximity, but maintained their distinct fungal associations. Similar patterns are characteristic of insect populations diversifying onto multiple hosts. We suggest that diversification and specialization of mycorrhizal associations have contributed to the rapid radiation of the Orchidaceae.