Leaf samples of endangered endemic orchid Calanthe izu-insularis Ohwi & Satomi collected at the time of full-bloom from two natural habitats on Mikurajima Island on (33°50′N, 139°37′E), ~200 km south of Tokyo, Japan, were examined for nine species of virus. Cucumber mosaic virus (CMV) was detected by reverse transcriptase–polymerase chain reaction (RT–PCR) and hybridisation in 4 of the 104 leaf samples from different plants of C. izu-insularis. Five plants were removed from their natural habitat and cultivated in a greenhouse. Concentrations of detectable CMV in these plants increased and CMV was detected in all five plants after 2 weeks of cultivation. However, after an additional 10 weeks of cultivation, CMV was not detected in any of the plants. Thus, it seems possible that almost all of the plants of this species in their natural habitat might harbour CMV at concentrations that are lower than the limit of detection by RT–PCR and hybridisation. The importance of these results for the conservation in situ is discussed.