The orchid symbiotic fungi were isolated and identified from the roots of Korean native orchids using modern molecular techniques. The selected isolates were segregated into several groups based on microscopic observations and PCR RAPD results, and symbiosis responses were different for the different fungi on the various plant species. All fungi isolates selected stimulated the root growth for all orchid species tested, and some affected the shoot growth of the Cymbidium temperate orchid.The five fungi 18s rDNA sequences were analyzed using BLAST. Based on the tested different characteristics, the fungal isolates were segregated into three groups.Two of these three symbiotic isolate groups were confirmed as Rhizoctonia repens (P01) and Rhizoctonia endophytica var. endophytica (P02).The patterns of the dendrograms made based on sequences of 18s rDNA were consistent with patterns of dendrograms obtained from the plant responses, but not consistent with the polymorphisms indicated by PCR RAPD. The fungal isolates collected from C. goeringii, a Korean native orchid, were different from plant pathogenic species of Rhizoctonia and Fusarium, well known as a soil borne disease. Also, the techniques to distinguish the symbiotic isolate from the pathogenic fungus was developed by using the PCR RAPD reacted with the primers employed.