Cistanche deserticola is an important medicinal plant in Mongolia. Despite its significant role in local healing systems, little traditional knowledge had been reported. The present study investigated folk names of C. deserticola and other species of the same community in Umnugobi Province, South Gobi region of Mongolia, based on ethnobotanical approaches. The high correspondence between folk names and scientific names of plant species occurring in Cistanche-associated community shows the scientific meaning of folk nomenclature and classification in Mongolia. The Mongolian and folk names of plants were formed on the basis of observations and understanding of wild plants including their morphology, phenology and traditional uses as well. Results from this study will support the conservation of C. deserticola itself, a rare and endangered plant species listed in the Monglian Red Data Book. Our documentation of folk nomenclature based on 96 plant species in the Cistanche community, as a part of traditional knowledge associated with biodiversity, will be very helpful for making strategy of plant biodiversity conservation in Mongolia.