Floral mutants display various deviant phenotypes and, as such, they are appropriate material with which to address the origin and the building of morphological variation. To identify the pivotal developmental stages at which floral variation may originate and to infer the putative associated genetic causes, we studied abnormal flowers in nine cultivars of Aquilegia and Delphinium of Ranunculaceae, a family displaying a high range of floral diversity. Wildtype flowers of the two genera are pentamerous and spurred, but they differ in their overall symmetry (actinomorphy vs. zygomorphy). Floral morphology of their cultivars at different developmental stages up to anthesis was observed, and the putative identity of the perianth organs and vascularization was inferred. Our results show that in the floral mutants in both genera, phyllotaxis was generally conserved, whereas floral organization, vascularization and symmetry were modified. Most of the morphological and anatomical deviations impacted the perianth, including organ number, identity and (spur) elaboration, and also led to the formation of mosaic organs. We hypothesized that the phenotypes of floral mutants in Aquilegia and Delphinium result from genetic alterations affecting frontiers between sets of organs of different identity, homeosis and length of floral meristem activity.