Gomphrena marginata Seub. (Amaranthaceae) is an endemic species from Brazilian campos rupestres with a fructan accumulating underground reserve system. Analyses of high performance anion exchange chromatography (HPAEC–PAD) revealed the presence of the soluble carbohydrates glucose, fructose, sucrose, 1-kestose, 6-kestose, nystose and fructans with degree of polymerization (DP) up to approximately 40 fructose units. Data of 1H and 13C Nuclear Magnetic Resonance (NMR) spectroscopy, including Heteronuclear Single-Quantum Correlation (HSQC) and Heteronuclear Multiple-Bonds Correlation (HMBC) showed the presence of β (2,6) linkages, characteristic of the linear molecule of levan-type fructan(2,6). These results confirmed previous studies suggesting that the reserve carbohydrate in the underground system of this species was levan-type fructans, similar to that of G. macrocephala. Structural analyses of the thickened underground system using light microscopy revealed a mixed origin system consisting mainly of a gemmiferous tuberous root with the upper region formed by short branched stems, both presenting vascular cylinders with unusual growth patterns. Fructan spherocrystals were visualized under polarized light and scanning electron microscopy (SEM) mostly in the cortex and vascular cylinder in both thickened stem and root. In addition to data reported in the literature concerning the occurrence of fructans in the Amaranthaceae, the results presented here suggest that fructans are a trait in this family while the levan-type fructan prevail in Gomphrena species.