This work represents an exploration of the ecological, evolutionary, and molecular mechanisms involved in the diversification of floral form in Achimenes---a colorful and diverse lineage containing 26 species, with centers of diversity in Mexico and Central America. Using an evolutionary-developmental based approach, we sequenced and analyzed the floral transcriptomes of 12 species at multiple developmental time points. These datasets were used to explore how patterns of gene expression, phylogenomic discordance, and co-expression network connectivity contribute to floral diversification in Achimenes. In the first chapter, we sequenced and characterized the floral transcriptomes of four species of Achimenes and examined patterns of gene expression during three stages of flower development. We found complex patterns of gene expression in the anthocyanin and carotenoid biosynthetic pathways that corresponded to different floral forms, identified candidate genes for corolla spur development, and detected numerous floral developmental genes under positive selection. The second chapter focuses on a phylotranscriptomic reevaluation of relationships in Achimenes while also examining patterns of recent gene flow. We sequenced the floral transcriptomes in an additional eight species and found moderate to high support for two distinct clades in the genus. Examination of gene orthologs found high levels of phylogenetic discordance due to introgression and incomplete lineage sorting. In addition, we documented two cases of recent introgression within two species pairs that are sympatric and share pollinators. The final chapter focuses on the construction of gene co-expression networks to examine how gene expression, network topology, and evolutionary rates interact. We found that while overall gene expression among Achimenes varied significantly in a clade- and pollination syndrome-specific manner, co-expression network modules were strongly associated to bee-, butterfly-, or hummingbird-pollination syndromes. We showed that genes with fewer connections in the periphery of the co-expression networks have higher evolutionary rates and are overrepresented by differentially expressed genes, while network cores remain strongly conserved. We discuss the significance of these patterns for floral diversification.