The MADS-box genes form a large family of pan-eukaryotic transcription factors that are involved in various aspects of plant growth and development, particularly reproduction. To understand the extent of their conservation and divergence in the emerging model genus Aquilegia L. (Ranunculaceae), we have annotated 47 MADS-box containing loci from the recently released hybrid A. coerulea E. James ‘Origami' genome sequence. Phylogenetic analysis of these sequences along with those previously identified from Arabidopsis (DC.) Heynh. and Oryza L. demonstrates that we were able to recover members of all major subfamilies with the exception of clear Mβ representatives. The evolution of the Aquilegia type I loci is similar to what has been observed for other angiosperms in exhibiting relatively recent gene radiation events. In contrast, the type II loci are distributed across 12 subfamilies that were established before the diversification of the angiosperms. Overall, expressed sequence tag (EST) data exist for 20 of these loci; further characterization of gene expression patterns will be an important next step. This characterization of Aquilegia MADS-box transcription factors thereby lays the foundation for many crucial studies on the development and evolution of Aquilegia as well as the conservation of function across the MADS-box gene family.