Transcription factors are key regulators of plant development. One of the major groups of transcription factors is the MADS-box family, of which at least 80 members are encoded in the Arabidopsis genome. In this study, 23 members of the petunia MADS-box transcription factor family were investigated by Northern hybridisation, phylogenetic and yeast two-hybrid analyses. Many of the genes characterised appeared to have one or more close relatives that shared similar expression patterns. Comparison of the binding interactions of these proteins revealed that some show similar interaction patterns, and hence are likely to be functionally redundant. From an evolutionary point of view, their coding genes are probably derived from a recent duplication event. Furthermore, protein-protein interaction patterns, in combination with expression patterns and phylogenetic classification, appear to offer good criteria for the identification of functional homologues. Based on comparison of such data between petunia and Arabidopsis, functions can be predicted for several MADS-box transcription factors in both species.