Several changes in climate and geology influenced the formation of the Amazon landscape as we know it today, with episodes of isolation and reconnection of previously continuous areas, and population expansion and contraction. Seasonally flooded areas comprise around 840,000 km2 of heterogeneous and dynamic regions, which shrink and expand during dry and rainy periods. They are ecologically divided according to the influence of white water rivers (varzea) and black or clear water rivers (igapó). The low number of investigations involving evolutionary, speciation and biogeography processes that influenced reptiles that occupy seasonally flooded areas leaves a gap in this knowledge and underestimates the level of diversity of this biota. The present work aims to understand the historical and evolutionary factors that generated the diversity of lizards that inhabit seasonally flooded and interconnected regions of Amazon rivers, as well as to investigate whether such species present cryptic diversity and whether they follow patterns proposed in hypotheses already postulated. For this, two species will be investigated: Neusticurus bicarinatus, Varzea bistriata and Uranoscodon superciliosus with a low-coverage whole genome sequencing for phylogenetic relationships, Bayesian cluster analyses, genetic diversity, divergence time and demographic reconstructions. Paleo-Distribution Modeling will also be carried out to test the hypothesis of past climate fluctuations in the diversification of U. superciliosus. Based on patterns already observed for the fauna of these environments, it is expected to find a scenario with genetic structure and cryptic diversity with diversification between the late Neogene and Quaternary, possibly linked to climate changes in the Plio-Pleistocene influencing the dynamism of the floodplain and consequent expansion population, distribution breakdown and isolation.