Orchids require a mycorrhizal relationship for seed germination. Many mycorrhizal fungi are in the form-genus Rhizoctonia, with teleomorphs in the genera Ceratobasidium, Tulasnella, Thanatephorus and Sebacina. So far there are very few reports of orchid mycorrhizal fungi in Colombia. The objectives of the present study were to isolate mycorrhizal fungi of orchids from different habitats in Colombia, and identify them by counting nuclei in young hyphae and sequencing the ITS region of nuclear ribosomal genes. We identified 12 isolates from 8 plants of different species of orchids. BLAST searches in GenBank and binucleate cellsplaced all isolates in the genus Ceratobasidium. The results suggest that this genus is associated with a wide variety of orchids from various habitats in Colombia. However, the consistency of the association raise questions about the pathogenicity of mycorrhizal Ceratobasidium on other plants, and their potential for biocontrol of pathogenic fungi in crops such as rice.