The origin and evolution of the perianth remains enigmatic. While it seems likely that an undifferentiated perianth consisting of tepals arose early in angiosperm evolution, it is unclear when and how differentiated perianths consisting of distinct organs, such as petals and sepals, arose. Phylogenetic reconstructions of ancestral perianth states across angiosperms have traditionally relied on morphological data from extant species, but these analyses often produce equivocal results. Here we describe the use of developmental genetic data as an additional strategy to infer the ancestral perianth character state for different angiosperm clades. By assessing functional data in combination with expression data in a maximum likelihood framework, we provide a novel approach for investigating the evolutionary history of the perianth. Results of this analysis provide new insights into perianth evolution and provide a proof of concept for using this strategy to explore the incorporation of developmental genetic data in character state reconstructions. As the assumptions outlined here are tested and more genetic data are generated, we hope that ancestral state reconstructions based on multiple lines of evidence will converge.