In many germinating orchids that rely on fungal partners for their nutrition, fungal diversity decreases during development. We document this pattern in the in situ development of Dendrobium moniliforme, where the diversity of cultivable Tulasnella species drops from the early germinating stage (6 Tulasnella species) to that of emergence of the second leaf (2 species), with species discontinuance and no new species appearing. We investigated the functional aspects of this decay by germinating seeds in vitro with the different strains available and observed, over 60 and 120 days, a perfect match between the stages at which Tulasnella spp. occur in situ and the ability to support in vitro development to this stage. The taxonomic bottleneck during germination may result, at least in D. moniliforme, from inability of the fungus to support seedling growth beyond a specific stage. Moreover, the isolated Tulasnella strains that best supported D. moniliforme development did not cluster together phylogenetically. Thus, the interaction between partners, rather than intrinsic fungal traits, may be involved in bottleneck of fungal symbionts during orchid germination.