SPECIATION is the process whereby populations acquire sufficient genetic differences to become reproductively isolated(1). Since Darwin it has been recognized that the tempo and mode of speciation are greatly influenced by the number and magnitude of genetic changes required for reproductive isolation(2-6), but detailed genetic studies have been limited to a few taxa such as Drosophila(7). Genome mapping techniques now widely adopted in plant(8,9) and animal(10,11) breeding make it possible to investigate the genetic basis of reproductive isolating mechanisms in natural populations. Here we use this approach to map eight floral traits in two sympatric monkeyflower species that are reproductively isolated owing to pollinator preference by bumblebees or hummingbirds. For each trait we found at least one quantitative trait locus accounting for more than 25% of the phenotypic variance. This suggests that genes of large effect can contribute to speciation.