A transition in flower color accompanying a shift in pollinator guilds is a prominent and repeated adaptation in angiosperms. In many cases, shifts to similar pollinators are associated with similar flower-color transitions. The extent to which this parallelism at the phenotypic level results from parallel changes at the biochemical, developmental, and genetic levels, however, remains an open question. There have been few attempts to determine whether parallelism at these lower levels results from mutation bias or fixation bias of different classes of mutation. We address these issues by examining the biochemical, developmental, and genetic changes that have occurred in red-flowering species of the Mina lineage of morning glories (Ipomoea) and compare these to the changes reported for I. horsfalliae, which has independently evolved red flowers. Using transgenic techniques, we demonstrate that the transition from blue to red flowers in Mina species is due primarily to down-regulation of the enzyme flavonol-3′-hydroxylase (F3′H) in flowers but not in vegetative tissues, and that this down-regulation is at least partly due to cis-regulatory change in the gene for F3′H. These changes are similar to those exhibited by I. horsfalliae, indicating parallelism at the biochemical and developmental levels, and possibly at the genetic level.