Orchids generally require a symbiotic fungus to complete their life cycle and thus characterization and identification of endomycorrhiza is essential. The most common mycorrhizal fungi of orchids belong to the genera Ceratobasidium, Sebacina, Thanetophorus, and Tu/asnella of Basidiomycota. The present study describes endophytic fungi from the roots of Papilionanthe subulata (Willd.) Garay, Rhynchostylis retusa (L.) Blume, and Taprobanea spathulata (L.) Christ, the three epiphytic orchids of Western Ghats. Five endophytic fungi were isolated from anchored roots, characterized morphologically and designated as Vs1,Vs2, Rr, Ps1, and Ps2. They were morphologically similar to that of the form genus Rhizoctonia and were binucleate in their vegetative hyphae and monilioid cells. Sequencing of ITS region and phylogenetic analysis revealed that Rr, VS1, and VS2 have close similarity to Ceratobasidium sp. while Ps1 and Ps2 with Tufasnella. Based on sequence similarity, Vs1 and Vs2 were assigned the species status Ceratobasidium lantanae-camarae and C. gomesae respectively and are new report from India. Other three isolates did not clad with any described species having sequences in the NCBI database.The sequences of the isolates were deposited in NCBI Genbank with the accession numbers, Rr_lTS OL374043, VS 1_ITS0L374050, VS2_ITSOL374052, PS1_ITS0L374163, and Ps2_ITS0L374168 respectively. The identified isolates are members of Ceratobasidiaceae or Tulasnellaceae and thus have symbiotic potential for further characterization and evaluation.