The formation of hybrids among closely related species has been observed in numerous plant taxa. Selection by pollinators on floral traits can act as an early reproductive isolating barrier and may be especially important when there is overlap in distribution and flowering time. In this study, we use Quantitative Trait Locus (QTL) mapping based on 293 codominant SNP markers in an F2 population (n = 328) to assess the size, magnitude, and location of the genetic regions controlling floral traits known to be important for pollinator attraction in 2 species of Lousiana Irises, Iris fulva and Iris hexagona. We also evaluate correlations among F2 traits and identify transgression in the hybrid population. Overall, we observe that differences in most floral traits between I. fulva and I. hexagona are controlled by multiple QTLs and are distributed across several linkage groups. We also find evidence of transgression at several QTL, suggesting that hybridization can contribute to generating phenotypic variation, which may be adaptive in rapidly changing environments.