Background: Orchids are highly dependent on mycorrhizae for survival and growth. Traditionally, to obtain orchid mycorrhizal fungi (OMFs) for plant growth, fungi have been isolated from the roots of mature wild plants; however, the species of OMF may change as the plants undergo different developmental stages. In this study, we developed the idea of using in situ seedling baiting to capture seedling growth-promoting fungi from Dendrobium officinale, an overcollected medicinal orchid in China.Results: In vitro-produced seedlings of D. officinale were transplanted into their original habitats, and newly established roots of well-growing seedlings were sampled for fungal isolation. Roots were sampled at 6 different times over one year, and five Tulasnella species and one Fusarium species were obtained and identified morphologically and molecularly. The ability to promote seedling growth was tested in three Tulasnella species TPYD-1, TPYD-2 and TPYD-3, with high isolation frequencies by inoculation onto in vitro-produced D. officinale seedlings. Although the three fungi were closely related species and clustered together in the phylogenetic tree, they showed different efficiencies in promoting D. officinale seedling growth. Tulasnella TPYD-2 showed a strong ability to promote seedling growth and could be selected for use in restoration plantings of D. officinale.Conclusions: Our results suggest that using an in situ seedling baiting technique could be an efficient way to obtain seedling growth-promoting fungi, and this approach could have broad applications in orchid mycorrhiza studies and orchid conservation.