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The purpose of this study was to gather ethnopharmacological information on plants used by the pastorals of southeastern Iran. The relationships between ecological value of the plant species and ethnobotanical indices were investigated. The loss of medicinal plants and its effective factors were also determined under nomadism and sedentary pastoralism. Ethnopharmacological information of plants was collected through interviews with 85 local people including nomads (43%) and sedentary pastorals (57%). Ethnobotanical indices including relative frequency of citation (RFC), relative importance (RI), cultural value (CV), and use value (UV) were estimated. Canopy cover and density of plant species were measured at 60 sampling plots in the exclosure, nomadic rangelands and sedentary pastorals rangelands. The Importance Value Index (IVI) and Relative Loss Index (RL) were estimated for both nomadic and sedentary pastoral rangelands. Pearson correlation coefficient was used to investigate the relationship between ethnobotanical indices and IVI of plant species. The Bayesian networks was used to investigate the relationship between ethnobotanical indices and plant species loss. In total, 156 medicinal plant species of 50 families were identified in the region by locals. Positive correlation was observed between ethnobotanical indices (RFC and RI) and ecological index (IVI). The mean decline of the ecological importance of medicinal species in sedentary pastoral rangelands was approximately three times higher than in nomadic rangelands. Bayesian networks showed that cultural value, seed exploitation and aerial parts exploitation had direct relationships with species loss in both nomadic and sedentary pastoral rangelands. Bunium persicum, an ecologically and socially important species, had been extensively harvested (more than 60%) in the both nomadic and sedentary pastoral rangelands, making it a priority species in future conservation programs. Medicinal plants had high ecological value and were severely exploited, threatening sustainability of arid and semiarid ecosystems. Local pastorals not only use medicinal plants as herbal remedies but also consider them as a source of income. Popular plants with multiple medicinal uses were more susceptible to loss. Higher medicinal knowledge of pastorals did not help to mitigate medicinal plant loss, requesting new plans to aware them to the circumstances that often leads to species removal from community. Given the importance, abundance and widespread use of medicinal plants, further studies can provide a basis for their conservation and for identifying new therapeutic effects of plants in the region.