The cerrado rupestre is a physiognomy of the Cerrado biome with a prominent ground layer. It is characterized by rocky outcrops; acidic, nutrient-poor soil; and water shortage due to climatic seasonality. Species of this biome have several mechanisms to survive these adverse conditions. This study aimed to investigate morpho-anatomical characteristics and soluble carbohydrates in underground systems of Apopyros warmingii and Ichthyothere terminalis (Asteraceae), and to evaluate the potentially adaptive roles of these structures under the environmental stressors of the cerrado rupestre. Samples of underground organs were fixed, dehydrated in graded ethylic ethanol, embedded in historesin, and sectioned. Qualitative and quantitative analyses of soluble carbohydrates were performed in distinct portions of the underground systems. Thickened underground systems of both species are composed of stem and root portions with buds in the proximal region. Vascular and cortical parenchymas are abundant and accumulate inulin, which can be visualized as spherocrystals. Secretory structures have lipophilic secretion. High fructan amounts in the parenchyma indicate their use to support resprouting. These carbohydrates may be mobilized to meet the increased demands of phenology and abiotic factors. Secretory structures and sclereids in both species and raphides in A. warmingii may assist the protection of the underground system against herbivores.