The understanding of diversification of intraspecific lineages can shed light on speciation processes and ultimately biogeographic patterns across multiple spatial and temporal scales. In this dissertation I investigated the geographical and ecological factors promoting diversification across the South American dry diagonal biomes (i.e. Cerrado, Chaco, and Seasonally Dry Tropical Forests - SDTFs), through a coupled approach between multilocus phylogeographic and geospatial methods, in the larger context of interpreting the consequences of the resulting patterns for the conservation of biodiversity and evolutionary processes. In Chapter 1 I evaluate biogeographic hypotheses previously proposed and emphasize that the dry diagonal biomes are particularly biodiverse and biogeographically complex, but poorly studied and under protected. I also propose testable predictions for the subsequent chapters and future diversification studies. In the subsequent chapters I adopt a biodiversity prediction approach based on estimating palaeodistributions and habitat stability surfaces to formulate and test spatially explicit diversification hypotheses based on squamate richness and phylogeography. In Chapter 2 I identify historically stable areas of SDTFs and in Chapter 3 I found that the historical climatic stability is a good predictor of Cerrado squamate richness. In Chapter 4 I use a multilocus dataset to estimate the phylogenetic relationships among described species of the lizard genus Phyllopezus (Phyllodactylidae), distributed across the ‘dry diagonal’ biomes. In Chapter 5 I used a dense sampling design focused in the species complex P. pollicaris (more individuals, localities, and markers), and coalescent phylogeographic methods to test the relative influences of Tertiary geomorphological vs. Quaternary climatic events on diversification in this lizard. I found unprecedented levels of cryptic genetic diversity, deep phylogeographic structure, and diversification dating back to at least the Neogene with persistence across Quaternary fluctuations. My dissertation emphasizes that patterns of diversification across the ‘dry diagonal’ biomes are much more complex than previously proposed and reflect the primary influence of geologically old processes. Evidence of allopatric and ecological speciation between lineages that coincide with genetic clusters associated with each of the biomes, contradicts early views that the biomes would have a shared diversification history. These patterns illustrate that low-vagility complexes, characterized by strong structure and pre-Pleistocene divergences, represent ideal radiations to investigate broad biogeography of associated biomes. Future studies should investigate patterns of temporal and spatial congruence across co-distributed taxa, and integrate morphological and further ecological data to refine species limits, taxonomy, and patterns of trait evolution across these radiations.