Evidence is accumulating for specialized yet evolutionarily dynamic associations between orchids and their mycorrhizal fungi. However, the frequency of tight mycorrhizal specificity and the phylogenetic scale of changes in specificity within the Orchidaceae are presently unknown. We used microscopic observations and PCR-based methods to address these questions in three taxa of nonphotosynthetic orchids within the Hexalectris spicata complex. Fungal ITS RFLP analysis and sequences of the ITS and nuclear LSU ribosomal gene fragments allowed us to identify the fungi colonizing 25 individuals and 50 roots. Thanatephorus ochraceus (Ceratobasidiaceae) was an occasional colonizer of mycorrhizal roots and nonmycorrhizal rhizomes. Members of the Sebacinaceae were the primary mycorrhizal fungi in every Hexalectris root and were phylogenetically intermixed with ectomycorrhizal taxa. These associates fell into six ITS RFLP types labeled B through G. Types B, C, D, and G were found in samples of H. spicata var. spicata, while only type E was found in H. spicata var. arizonica and only type F was found in H. revoluta. These results provide preliminary evidence for divergence in mycorrhizal specificity between these two closely related orchid taxa. We hypothesize that mycorrhizal interactions have contributed to the evolutionary diversification of the Orchidaceae.