Unlike photosynthetic plants, several distantly related nonphotosynthetic plants are highly specialized toward their mycorrhizal fungi. It is unknown whether this specialization varies geographically or is influenced by the environment. We have investigated these questions in the nonphotosynthetic orchids Corallorhiza maculata and C. mertensiana by amplifying fungal internal transcribed spacer (ITS) fragments from widespread mycorrhiza samples and then discriminating putative fungal species using ITS restriction fragment length polymorphisms (RFLPs). Three fungal species were found across 27 plants representing seven populations of C. mertensiana; 20 species were found across 104 plants and 21 populations of C. maculata. All fungi belonged to the Russulaceae, an ectomycorrhizal family. Partitioning of Simpson’s diversity showed that 48% of the variance in occurrences of fungal species coincided with population boundaries in C. mertensiana, vs. 68% in C. maculata. This differentiation coincided with geography but not habitat in C. mertensiana. In contrast, likelihood ratio tests showed strong associations between fungal occurrence and both habitat and phenotype in C. maculata. For example, C. maculata populations growing under oaks had no fungi in common with nearby populations growing under conifers, and those above 2000 m had no fungi in common with those below 2000 m. However, plant genetic differentiation may underlie some of these patterns. C. mertensiana and C. maculata never shared fungal species, even when growing intermixed at the same site, demonstrating genetic control that was independent of habitat. Similarly, intermixed normal and pale-coloured variants of C. maculata had no fungal species in common. These results demonstrate fine-scale genetic influences and geographical mosaicism in a mycorrhizal interaction.