The two related Petunia species, P. axillaris and P. integrifolia, are sympatric at various locations in South America but do not hybridise. Divergent pollinator preferences are believed to be in part responsible for their reproductive isolation. The volume of nectar produced and several components of flower morphology might contribute to pollinator-dependant reproductive isolation. In this study, we aimed to identify the genetic changes underlying the quantitative differences observed between these two Petunia species in flower size and nectar volume. We mapped quantitative trait loci (QTL) responsible for the different phenotypes of P. axillaris and P. integrifolia in an inter-specific backcross population. QTL of small to moderate effect control the differences in flower size and volume of nectar. In addition, we observed strong suppression of meiotic recombination in Petunia, even between closely related species, which precluded a fine resolution of QTL mapping. Thus, our data suggest that flower size and nectar volume are highly polygenic. They are likely to have evolved gradually through pollinator-mediated adaptation or reinforcement, and are not likely to have been primary factors in early steps of pollinator isolation of P. axillaris and P. integrifolia.