Throughout the industrialized world, wetland species face the greatest risk of extinction from altered environmental conditions and loss of habitat. Manmade wetlands are often the only feasible strategy to provide habitat for these species. Wetland orchids are particularly susceptible to environmental degradation due to potentially limited availability of specialized pollinators and mycorrhizal symbionts. Here, we assess the fungal symbiont diversity of two orchid species, Habenaria radiata and Epipactis thunbergii, occupying three manmade wetlands in Hiroshima Prefecture, Japan to determine if orchids colonizing reconstructed habitats associate with a phylogenetically diverse or narrow suite of fungal symbionts. We collected three individuals each of H. radiata and E. thunbergii, respectively, growing at the first pond, six H. radiata from a second pond, and two E. thunbergii from a third pond. We identified fungal taxa using PCR and DNA sequencing techniques. Habenaria radiata associated with a phylogenetically diverse suite of fungi; in comparison, E. thunbergii associated with a phylogenetically narrow range of fungi dominated by the Tulasnellaceae. These common wetland orchid species readily colonize manmade wetlands, and we propose sampling soils for the presence of appropriate mycorrhizal fungi to determine limitations on orchid population regeneration due to mycorrhizal specificity.