Evolution sometimes repeats itself. The recurrent origin of forms and species exists across kingdoms, but we remain largely ignorant about its genetic causes. Here we use native Australian daisies from the genus Senecio to uncover the molecular basis of the parallel evolution of prostrate and erect forms, and the repeated evolution of reproductive isolation between them. We combine novel population genomic approaches and classical genetics with field experiments to trace the genes responsible for these traits. Our results will provide fundamental information on the genetic basis of plant speciation driven by natural selection, thus helping to fill a gap in our understanding of how species originate and adapt to novel environments.