Orchids require orchid mycorrhizal fungi (OMF) for seed germination and seedling establishment. Because of this obligate relationship, host species' occurrence, distribution, fitness and environmental features can be linked to the identity, specificity, and availability of their fungal partners. The ecology of OMF associated with the genus Vanilla, however, remains largely unknown, despite its pan-tropical distribution with approximately 120 species. We investigated the patterns of mycorrhizal association in four populations of V. trigonocarpa in Costa Rica, comprising three populations in the Pacific region and one in the Atlantic region separated by three mountain ranges. The closest and farthest populations were separated by 2 and 220 km respectively. Within each population, we sampled the epiphytic and terrestrial roots separately to identify the associated fungal communities, including OMF communities. We hypothesized: 1) Pacific populations will show greater similarity in their OMF communities when compared to the Atlantic population; 2) similarity in the OMF communities will decrease with increasing geographic distance between the populations; and 3) OMF communities associated with the epiphytic roots will be distinct when compared to the terrestrial roots, both within each population and for the orchid host as a whole. Sequencing the nuclear ribosomal internal transcribed spacer (nrITS) region yielded 65 OMF Operational Taxonomic Units (OTUs) from 107 root samples. Thirty of the 65 OTUs across all data were assignable to the family Tulasnellaceae representing 52% of all fungal sequences, followed by the family Ceratobasidiaceae (17 OTUs) and order Atractiellales (2 OTUs), represented by 19% RA each. When comparing the OMF communities of the two regions, PERMANOVA (p < 0.05), hierarchical clustering, and Principal Coordinate Analyses (PCoA) showed a clear separation of the two regions. Although Tulasnellaceae OTUs dominated the roots in each population, the composition of the OTUs was differentiated. The Atlantic population hosted 6 unique OTUs (3 Tulasnellaceae; 3 Ceratobasidiaceae) that together represented 72% of all sequences. The Pacific populations altogether hosted 5 OTUs (4 Tulasnellaceae; 1 Ceratobasidiaceae) that were not shared with the Atlantic population but were shared by the three Pacific populations. Regardless of their native provenance, a Mantel test showed that the four populations followed a distance-decay pattern between similarity in OMF communities and geographical distance (p < 0.05). Further, we also detected different OMF community compositions in the two root types within each population and when data from all populations were combined, supported by PERMANOVA (p < 0.05) and PCoA. While the Atractiellales (1 OTU) and Serendipitaceae (9 OTUs) collectively made up 91% of the OMF community in the epiphytic roots, 13 OTUs of the Tulasnellaceae and 5 OTUs of the Ceratobasidiaceae dominated the terrestrial roots with a combined relative abundance of 83%. Taken together, our first evidence of geographic-scale OMF community niches of Vanilla indicates the capacity of a hemi-epiphytic orchid with large photosynthetic biomass to have specialized mycorrhizal niches, which are further stratified vertically between the epiphytic and terrestrial roots. The distinct OMF communities of disjunct populations reveal specialization at local levels while associating with a wider pool of OMF across space.