Chrysolaena obovata (Less.) Dematt., a herbaceous Asteraceae species widely distributed across different Brazilian Cerrado physiognomies, bears underground organs, named rhizophores, that accumulate high concentrations of inulin-type fructans. These carbohydrates are recognized as beneficial soluble fibers for human health and are currently used in food and pharmaceutical industries. Considering that fructans, in addition to their economic potential, provide plants with greater tolerance to drought, heat and cold, it is important to understand whether their metabolism is conserved in natural populations. In this study, we investigated if the levels of genetic diversity in the studied populations allow selection of localities with high genetic base and high fructan content for future programs of in situ conservation and genetic improvement for inulin production. We characterized diversity, structure, and gene flow of seven natural populations from the Brazilian Cerrado, using nine microsatellite loci (SSR). In addition, we compared fructan composition between populations of different Cerrado phytophysiognomies. Overall, we found that C. obovata populations exhibited moderate levels of genetic diversity, low genetic differentiation, and high gene flow. This study identified two populations with lower genetic diversity (Santa Bárbara and Serra Dourada) than the remaining five, suggesting that greater attention should be given to conservation programs including these populations. Fructan metabolism is conserved in all populations, indicating that C. obovata is an important genetic resource with high potential for inulin production.