Flavonoids play many important roles in plants and their interactions with their environment. They are major components that control flower colors and seed coat coloring in legumes. Many of these pigments have been used as markers to study different biological and evolutionary processes within the legumes. Although several studies have been done on the flavonoid biosynthetic pathway which determines the flower colors of different species the connections between ecology, phenotype, and genetics have not been fully described yet. Pigmentation in Phaseolus is quite complex with many loci involved and interactions of these loci together can lead to different pigmentation in flowers and seed coats. The Sal gene is believed to control the salmon flower color in Phaseolus vulgaris and its presence coupled with other secondary gene loci can led to different colors and color patterns such as bicolored flowers. In our study, we have chosen to focus on the salmon flower color and cream-beige seed coat color. We have chosen to take an Ion torrent based shotgun sequences approach to survey the genetic diversity of this species with respect to currently sequenced legumes. Our aim is to provide a comparative analysis across these species as well as sequence for the entire flavonoid pathway to allow further targeted sequencing of Phaseolus varieties with a wide range of flower and seed coat colors.