Aim: Present Amazonian diversity patterns can result from many different mechanisms and, consequently, the factors contributing to divergence across regions and/or taxa may differ. Nevertheless, the river-barrier hypothesis (RBH) is still widely invoked as a causal process in divergence of Amazonian species. Here we use model-based phylogeographic analyses to test the extent to which major Amazonian rivers act similarly as barriers across time and space in two broadly distributed Amazonian taxa. Local: Amazon rainforest. Taxon: The lizard Gonatodes humeralis (Sphaerodactylidae) and the tree frog Dendropsophus leucophyllatus (Hylidae). Methods: We obtained RADseq data for samples distributed across main river barriers, representing main Areas of Endemism previously proposed for the region. We conduct model-based phylogeographic and genetic differentiation analyses across each population pair. Results: Measures of genetic differentiation (based on FST calculated from genomic data) show that all rivers are associated with significant genetic differentiation. Parameters estimated under investigated divergence models showed that divergence times for populations separated by each of the 11 bordering rivers were all fairly recent. The degree of differentiation consistently varied between taxa and among rivers, which is not an artifact of any corresponding difference in the genetic diversities of the respective taxa, or to amounts of migration based on analyses of the site-frequency-spectrum. Main conclusions: Taken together, our results support a dispersal (rather than vicariance) history, without strong evidence of congruence between these species and rivers. However, once a species crossed a river, populations separated by each and every river have remained isolated – in this sense, rivers act similarly as barriers to any further gene flow. This result suggests differing degrees of persistence and gives rise to the seeming contradiction that the divergence process indeed varies across time, space, and species, even though major Amazonian rivers have acted as secondary barriers to gene flow in the focal taxa.