The species within the now well-defined Arabidopsis genus provide biological materials suitable to investigate speciation and the development of reproductive isolation barriers between related species. Even within the model species A. thaliana, genetic differentiation between populations due to environmental adaptation or demographic history can lead to cases where hybrids between accessions are non-viable. Experimental evidence supports the importance of genome duplications and genetic epistatic interactions in the occurrence of reproductive isolation. Other examples of adaptation to specific environments can be found in Arabidopsis relatives where hybridization and chromosome doubling lead to new amphidiploid species. Molecular signals of speciation found in the Arabidopsis genus should provide a better understanding of speciation processes in plants from a genetic, molecular and evolutionary perspective.