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Abstract Speciation is a complex process typically accompanied by significant genetic and morphological differences between sister populations. In plants, divergent floral morphologies and pollinator differences can result in reproductive isolation between populations. Here, we explore floral trait differences between two recently diverged species, Gilia yorkii and G. capitata. The distributions of floral traits in parental, F1, and F2 populations are compared, and groups of correlated traits are identified. We describe the genetic architecture of floral traits through a quantitative trait locus analysis using an F2 population of 187 individuals. While all identified quantitative trait locus were of moderate (10–25%) effect, interestingly, most quantitative trait locus intervals were non-overlapping, suggesting that, in general, traits do not share a common genetic basis. Our results provide a framework for future identification of genes involved in the evolution of floral morphology.