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ABSTRACT In integrative distributional, demographic and coalescent (iDDC) modelling, a critical component is the statistical relationship between habitat suitability and local population sizes. This study explores this relationship in twoEnyaliuslizard species from the Brazilian Atlantic Forest: the high‐elevationE. iheringiiand low‐elevationE. catenatusand how this transformation affects spatiotemporal demographic inference. Most previous iDDC studies assumed a linear relationship, but this study hypothesises that the relationship may be nonlinear, especially for high‐elevation species with broader environmental tolerances. We test two key hypotheses: (1) The habitat suitability to population size relationship is nonlinear forE. iheringii(high‐elevation) and linear forE. catenatus(low‐elevation); and (2)E. iheringiiexhibits higher effective migration across populations thanE. catenatus. Our findings provide clear support for hypothesis (2), but mixed support for hypothesis (1), with strong model support for a nonlinear transformation in the high‐elevationE. iheringiiand some (albeit weak) support for a nonlinear transformation also inE. catenatus. The iDDC models allow us to generate landscape‐wide maps of predicted genetic diversity for both species, revealing that genetic diversity predictions for the high‐elevationE. iheringiialign with estimated patterns of historical range stability, whereas predictions for low‐elevationE. catenatusare distinct from range‐wide stability predictions. This research highlights the importance of accurately modelling the habitat suitability to population size relationship in iDDC studies, contributing to our understanding of species' demographic responses to environmental changes.