ABSTRACT Aim: To assess the effects of climate change on genetic lineages of Arabidopsis thaliana at the admixed population level by directly modelling genetic cluster membership values to predict potential genetic cluster memberships across the Iberian Peninsula. Location: Iberian Peninsula Methods: We used a dataset of 274 accessions structured in four genetic clusters as inferred from 250 nuclear single-nucleotide polymorphisms with Bayesian clustering methods. We predicted the change in percentages of genetic cluster membership at a population level and the changes in potential suitability across the study area by combining parametric (Beta regression) and non-parametric (Recursive trees) methods. Results: Climate change will affect genetic lineages of Arabidopsis thaliana differently. Genetic clusters GC1 and GC2 will suffer a substantive reduction of their respective suitable areas while GC3 and GC4 will expand northward. At the population level, except for GC4, the rest of the lineages will undergo a genetic turnover for many of their populations. Main conclusions: A. thaliana in the Iberian Peninsula will undergo a major internal genetic restructuring and range change due to climate change. Genetic lineages of Arabidopsis thaliana in the Iberian Peninsula will be affected differently which reinforce the need for taking into account intraspecific genetic variation when modelling species distribution. Despite limited predictive power of individual statistical models, the combination of distinct models can compensate this shortcoming.