Almost all orchid species depend on association with fungal partners. These fungal species facilitate orchid seed germination and promote growth and possibly stress tolerance in adult plants, both in the field and laboratory conditions. Codonorchis lessonii is a terrestrial orchid, endemic to southern Chile and Argentina with a currently unknown conservation status. Previous studies have reported Rhizoctonia-like fungi associated with C. lessonii in Argentina, but their fungal partners in Chilean populations are unknown. This study aims to characterize and isolate the mycorrhizal fungi associated with adult individuals of C. lessonii from three different populations in Central-South Chile. Root sections showing pelotons were used for the isolation and identification of the fungal taxa. Radial fungal growth was measured for all mycelial isolates. The presence of binucleate cells placed all isolates within the families Ceratobasidiaceae and Tulasnellaceae and the identification was confirmed by molecular analysis. Fungal isolates belonging to Ceratobasidiaceae grew at a higher rate than those from Tulasnellaceae. Phylogenetic analyses showed that different fungal partners associate with this orchid, suggesting relatively low specificity. The isolation and identification of the fungal partners of C. lessonii could help understand its ecology and contribute in future restoration and propagation initiatives for the species.