Duplicate genes may be retained by sub- and/or neofunctionalization through changes in gene expression and/or coding sequence, and therefore have the potential to contribute to the genetic robustness and diversification of an organism. In this study, two MADS-box genes were isolated from Taihangia rupestris, a core eudicot species belonging to the Rosaceae. Sequence and phylogenetic analyses revealed that they are clade members of the euAG and PLE lineages, respectively, and hence the two genes are named TrAG (Taihangia rupestris AGAMOUS) and TrSHP (Taihangia rupestris SHATTERPROOF). Southern blot analysis shows that TrSHP is a single-copy gene in the T. rupestris genome. In situ hybridization analyses show that both TrAG and TrSHP are mainly expressed in the stamens, carpels, and ovules. When the stamen primordia are firstly observed, TrAG is initially expressed in the floral meristem domain that will initiate stamens and carpels. In contrast, no TrSHP signal is observed at this developmental stage. At late stages of carpel development, TrAG expression is detected in the ovules, ovaries, and developing styles and stigmas, whereas TrSHP expression is tightly restricted to the ovules. The transgenic Arabidopsis plants containing 35S::TrAG and 35S::TrSHP, respectively, showed similar phenotypes, including homeotic conversions of sepals into carpelloid structures bearing ovules and petals into staminoid organs, and the fruits shattering prematurely along the dehiscence zone. In addition, the phenotype of the transgenic 35S::TrSHP Arabidopsis plants revealed that perianth abscission was inhibited. Yeast two-hybrid assays indicated that TrAG can interact with TrSEP3, whereas TrSHP cannot. The data suggest that the euAG and PLE paralogs, TrAG and TrSHP, may have subfunctionalized and/or neofunctionalized through changes in expression patterns and accumulating variations in the coding regions. Taking these findings together with those available expression and functional data from Arabidopsis and other species, we conclude that the compensatory ways vary among the euAG and PLE lineage pairs in eudicot species.