Disturbance alters the structure and dynamics of communities. Here, we examined the effects of seasonal flooding on the lizard community structure by comparing two adjacent habitats, a seasonally flooded and a non-flooded forest, in a Cerrado-Amazon ecotone area, the Cantão State Park, Tocantins state, Brazil. Despite the strong potential impact of seasonal flooding, the only significant environmental difference detected was more termite mounds in non-flooded forests. Species richness was significantly higher in the non-flooded forest. Colobosaura modesta, followed by Mabuya frenata and Anolis brasiliensis, were the only species that differed in number of captures between sites. Colobosaura modesta was exclusively found in the non-flooded forest, while Anolis brasiliensis was the most captured in the flooded forest. Mabuya frenata is indicated as an indicator species in the flooded forest, and Colobosaura modesta in the non-flooded forest. We found a significant association between lizard abundances and habitat characteristics, with flooding, canopy cover, and logs being the best predictors. A phylogenetic community structure analysis indicated a lack of structure in both lizard assemblages. Overall, we show that seasonal flooding can strongly impact species richness and species occurrence patterns, but not phylogenetic community structure. The Amazon-Cerrado transition is undergoing pronounced transformations due to deforestation and climate change. Despite being species-poor compared with central areas in Amazon or Cerrado, this ecotone harbors species with important adaptations that could hold the key to persistence in human-disturbed landscapes or during periods of climate change.Abstract in Portuguese is available with online material.