Floral traits such as flower size, shape, and pigmentation are major factors in pollination biology, providing cues for pollinator attraction or mechanisms for effective pollen transfer. To understand the evolutionary processes and the genetic mechanisms that drive adaptive morphologies, we investigate the genetic regulatory mechanisms that give rise to the wide diversity of floral traits across the genus Calochortus. The highly charismatic genus is an excellent model to investigate the genetic mechanisms underlying developmental evolution due to the high diversity of suites of traits or ‘floral syndromes’. The four floral syndromes are characterized by variation in trichome densities and placement on petals, diversity of flower size, a wide spectrum of floral pigments, and variation in floral posture (i.e., erect v nodding flowers). A three-pronged comparative transcriptomic approach using RNA-Sequencing data is employed to identify candidate regulatory genes expressed in floral tissue: 1) comparing expression patterns across three species at three developmental times points using a high quality reference transcriptome, 2) comparing expression patterns within each of three species across three developmental stages using species-specific transcriptomes, and 3) identifying ortho groups across six species and looking for signatures of selection on the coding regions of candidate genes identified from expression analyses. With this approach we can examine key players regulating the development of floral traits that have been recruited across floral syndromes and determine if key genes are similarly expressed during the same developmental stage across syndromes. If expression of candidate genes does not change across floral syndromes we can determine if there are structural changes in the genes associated with different phenotypes.