Species often harbour large amounts of phenotypic variation in ecologically important traits, and some of this variation is genetically based. Understanding how this genetic variation is spatially structured can help to understand species’ ecological tolerances and range limits. We modelled the climate envelopes of Arabidopsis thaliana genotypes, ranging from early- to late-flowering, as a function of several climatic variables. We found that genotypes with contrasting alleles at individual flowering time loci differed significantly in potential range size and niche breadth. We also found that later flowering genotypes had more restricted range potentials and narrower niche breadths than earlier flowering genotypes, indicating that local selection on flowering can constrain or enhance the ability of populations to colonise other areas. Our study demonstrates how climate envelope models that incorporate ecologically important genetic variation can provide insights into the macroecology of a species, which is important to understand its responses to changing environments.