Partially mycoheterotrophic plant species obtain organic carbon, via both photosynthesis and mycorrhizal symbiosis. In this study, we investigated the mycorrhizal fungi association and nutritional mode of Cheirostylis liukiuensis, which is suspected to be a partial mycoheterotrophic plant, due to its characteristic reduced underground organs, low-light growth environment, and some fully mycoheterotrophic species in the phylogenetically related genera. Molecular analysis of the dominant mycobiont and stable isotope analysis suggested that C. liukiuensis is a partial mycoheterotrophic plant predominantly associate with non-ectomycorrhizal Ceratobasidiaceae fungi. As examples of partial mycoheterotrophic orchids exploiting non-ectomycorrhizal rhizoctonia are still limited, this study provides valuable information on the nutritional modes of green orchids.