Flowers and leaves each represent suites of functionally interrelated traits that are often involved in species divergence and local adaptation. However, a major unresolved issue is how the individual component traits that make up a complex trait such as a flower evolve in a coordinated fashion to retain a high degree of functionality. We use a quantitative trait loci (QTL) approach to elucidate the genetic architecture of divergence in flower and leaf traits between sister species of Primulina depressa and Primulina danxiaensis, which are found sympatrically, but in contrasting microhabitats. We found that flower traits were controlled by multiple QTL of small effect, while leaf physiological and morphological traits tend to be controlled by QTL of larger effect. The observed floral integration, manifested by a high degree overlap in both individual trait QTL and QTL for principal component scores (PCA QTL), may have been critical for evolutionary divergence of floral morphology in relation to their pollinators. This overlap suggests that direct selection on only one or a few of the component traits could have caused substantial divergence in other floral traits due to genetic correlations, while the lack of QTL overlap between floral and vegetative traits suggests that these trait suites are genetically unlinked and can evolve independently in response to different selective pressures corresponding to their distinct functions.