Eupomatia (Magnoliales, Eupomatiaceae) a genus of shrubs and trees, has flowers that bear a calyptra, an unusual organ that encloses the floral bud. The structural homology and evolutionary derivation of the calyptra are unknown, although some have proposed that it is a bract, while others favor a derivation from the perianth. To address the evolutionary origin of the calyptra, we isolated, sequenced, and characterized the expression of A-, B-, and E-class MADS-box homologues from Eupomatia bennettii and a close relative, Magnolia grandiflora (Magnoliaceae). The expression patterns of organ identity genes in floral organs of Eupomatia and Magnolia were very similar. However, the expression patterns of these MADS-box genes indicated that the ABC model is not strictly applicable to either Eupomatia or Magnolia. For example, A-class homologues were expressed in carpels and leaves of both Eupomatia and Magnolia. In the calyptra, expression levels of B- and E-class homologues were low and almost identical to those observed in leaf tissue. In contrast, high levels of expression for B- and E-class homologues were observed in the stamens, staminodes, and carpels. These gene expression data agree with recent developmental data and the interpretation of the calyptra as a bract. We also report the presence of various forms of alternatively spliced mRNAs in the cDNA pool from floral organs, and the implications of these mRNAs are discussed.