Resource partitioning among small mammals mostly occurs through segregation on both food and spatial dimensions. Structurally distinct forests of the highly seasonal Brazilian savanna (Cerrado), such as the cerradão (dry woodland forest-WF) and the gallery forest (forests that surround water courses-GF), allow comparisons of small-mammal resource partitioning between areas with similar assemblages but distinct structural complexities. Using 13C and 15N stable isotopes, we described isotopic assimilation and compared the partitioning of isotopic niche of small mammals from both forest types. Considering the higher plant diversity and complexity of the GF, we expected a broader overall range of the isotopic niche for the assemblage and higher specific niche specialization in this forest type in comparison with the WF. Moreover, as small mammals are generalists and plastic foragers, we predicted that species that occur in both forest types would show a broader niche breadth in WF due to its lower complexity and potentially higher variability in resource availability along the year. The WF assemblage presented higher δ15N range, increased general isotopic niche and decreased overlap in comparison to the GF assemblage, contradicting our initial expectation. These patterns indicate that the assemblages mirrored differences in plant isotopic signatures between forests. Rodent species occurring in both forests (3 spp) presented larger isotopic niche amplitude in GF, whereas marsupials (2 spp) did not show this same pattern, suggesting a larger plasticity on the use of food resources by rodents. Both resource availability and diversity influenced isotopic assimilation by small mammals in Cerrado forests.