Abstract The Colombian Orinoquia region is characterized by a high diversity of mammals, which is associated with complex ecosystems that include large extensions of Neotropical savannas (known locally as “Llanos Orientales”). Despite accelerated anthropogenic transformations in savanna ecosystems, the knowledge to design effective conservation strategies, such as the distribution of mammal assemblages, is still lacking for this region. In this paper, we evaluate if assemblages of medium and large mammals (i.e., species richness, relative abundance and the contribution of the different trophic guilds) are homogeneous across the Colombian Llanos by comparing three savanna ecosystems: floodplains savannas associated with an Andean river, aeolian floodplains savannas and highland savannas. After a sampling effort of 3,150 camera trap/days, we recorded 16 mammal species from the three savanna ecosystems. We compared the three assemblages and their constituent trophic guilds by ANOSIM and SIMPER non-parametric permutation tests. The three assemblages differed in composition, structure and trophic guilds. The floodplains savannas, associated to an Andean river, present the highest diversity, contrastingly, the high-plain associated with the Guyanese Shield presents the lowest diversity. This pattern could be explained due to the greatest floristic diversity, complex vegetation structure and more fertile soils present in the riparian forests of the floodplains savannas, despite being the most anthropogenically transformed. The carnivores were the most variable category and herbivores were the most abundant. Our results show that the diversity of medium and large mammals is heterogeneously distributed in the Colombian Llanos. Therefore, it is necessary to implement targeted conservation strategies according to the characteristics, local fragility of each ecosystem in the territory and each species response by local conditions.