Species‐Specific Responses to Paleoclimatic Changes and Landscape Barriers Drive Contrasting Phylogeography of Co‐Distributed Lemur Species in Northeastern Madagascar

River barriers have long played a central role in diversification models of tropical regions, including the exceptionally biodiverse island Madagascar. Although their role is best understood by integrating additional factors such as elevation and the ecological niche of a species, empirical studies integrating these variables remain rare. We used restriction site-associated DNA sequencing to assess the combined effect of rivers, topography, climate and forest cover on the distributions and diversity of four Microcebus and two Avahi species (Primates, Lemuriformes) in northeastern Madagascar. We inferred population structure, gene flow and genetic diversity, and assessed the association of these ecogeographic variables and genetic differentiation using isolation-by-resistance models. Our results show that significant differences in genetic diversity and connectivity among species can be explained by species-specific responses to landscape features and phylogeographic histories. Specifically, rivers present general barriers to gene flow, but dispersal between inter-river systems is possible via high-elevation headwater regions. While this led to high connectivity and genetic diversity in M. lehilahytsara and A. laniger, gene flow among M. jonahi populations is limited by low climatic niche suitability at higher elevations. Moreover, the more restricted distributions of M. macarthurii, M. simmonsi and A. mooreorum likely resulted from refugial dynamics and sea level fluctuations leading to allopatric divergence and microendemism. Together, the findings illustrate how ecological differences among species and temporal landscape dynamics mediate the role of rivers as dispersal barriers. They also highlight the importance of prioritising river headwaters and topographically complex regions, which were shown to promote connectivity, in conservation efforts.