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Orchids exhibit varying specificities to fungi in different microbial environments. This pilot study investigated the preference of fungal recruitment during symbiotic germination of <i>Epidendrum radicans</i> Pav. ex Lindl. Two different orchid substrates were used for ex situ seed baiting: pine bark and rotten oak leaf, with Basidiomycota and Ascomycota as the respective dominant groups. Both substrates promoted seed germination, with a higher protocorm formation rate on pine bark (65.75%). High-throughput sequencing characterized the fungal communities of germinated protocorms. Basidiomycota was the dominant group in protocorms that symbiotically germinated on both substrates. The family-level community structures of endophytic fungi in protocorms that symbiotically germinated on both substrates were close to those of protocorms that germinated in vitro on MS1 medium. For protocorms, the dominant fungal groups recruited from substrates differed at the genus level; from pine bark, they were genera belonging to unclassified Sebacinales (41.34%), <i>Thanatephorus</i> (14.48%) and <i>Fusarium</i> (7.35%), while, from rotten oak leaf, they were <i>Rhizoctonia</i> (49.46%), <i>Clitopilus</i> (34.61%), and <i>Oliveonia</i> (7.96%). Four fungal isolates were successfully obtained and identified as belonging to the family Tulasnellaceae, genera <i>Ceratobasidium</i> and <i>Peniophora</i>, which could promote seed germination to the seedling stage. The data indicate that endophytic fungi for <i>E. radicans</i> germination on two different substrates are affected at the genus level by the substrate, with a degree of specificity at the family level.