Plants that produce dust seeds can recruit fungi to meet their earliest requirements for carbon and other nutrients. This germination strategy, termed initial mycoheterotrophy, has been well investigated among the orchid family, but there are numerous other plant lineages that have independently evolved mycoheterotrophic germination strategies. One of these lineages is the tribe Pyroleae (Ericaceae). While the fungi associated with mature plants in Pyroleae have been fairly well documented, their mycobionts at the germination and seedling stages are largely unknown. Here, we use an in situ seed baiting experiment along with molecular fingerprinting techniques and phylogenetic tests to identify the fungi associated with seedlings of two Pyroleae species, Pyrola chlorantha and Orthilia secunda. Our results indicate that similar to adult plants, Pyroleae seedlings can associate with a suite of ectomycorrhizal fungi. Some seedlings harboured single mycobionts, while others may have been inhabited by multiple fungi. The dominant seedling mycobiont of both Pyroleae species was a fungus of unknown trophic status in the order Sebacinales. This taxon was also the only one shared among seedlings of both investigated Pyroleae species. We discuss these results juxtaposed to orchids and one additional Pyrola species in the context of ontogenetic shifts in fungal host specificity for mycoheterotrophic nutrition.