Pleistocene climate fluctuations are known to be an important driving force in biological differentiation. Despite Sundaland’s high levels of biodiversity and the important impact Pleistocene climate fluctuations have had on Sundaic landmass connectivity and topography, studies of the impact of those fluctuations on differentiation in Sundaic species are scarce. Recent studies have shown complex patterns of bioacoustics and genetic variation among bird populations of different landmasses in Sundaland, suggesting that some of those populations may in fact no longer experience gene flow between one another despite recurrent land bridges connecting their ranges. Babblers (Timaliidae) are highly sedentary denizens of the undergrowth of Southeast Asian rainforests in which great regional bioacoustic variation has previously been reported. As such, they are an ideal model to study the mechanisms that have led to biological differentiation across Sundaland. Here, we use genome-wide sequence data to assess patterns of diversification and gene flow among populations from different parts of the Sundaic region. Pleistocene climate fluctuations may have affected population connectivity differently depending on species ecology. We therefore conducted a comparison between a forest-dependent babbler complex (Cyanoderma erythropterum) and an edge-tolerant babbler complex (Mixornis gularis).