Flower formation is one of the main developmental stages in the life cycle of flowering plants that can be used as a model system to elucidate the molecular mechanics that control the developmental process in plants. In the present study, we investigated the floral homeotic and MADS box genes in the polygamadioecious tree Garcinia indica. The differential gene expressions of floral homeotic and MADS box genes in male, female, bisexual flowers, and floral organs such as sepal, petal, stamen, and carpel were studied by employing quantitative real-time, PCR-based assays. Of nine differentially expressed floral genes of the MADS box class, AGL11, the master control gene of ovule identity was found to be expressed 2-fold higher in female carpel whereas the ribosome protein involved in ovule development showed 2×106-fold high expression in the female carpel. The hierarchical clustering grouped these genes into four major clusters: cluster I comprised AGL11, AG, and PMADS2, cluster II comprised AP3 and AGL9, cluster III comprised SEP1 and ELFB, and cluster IV comprised AG pathway and ribosome protein. The clustering found was correlated with the quantitative and qualitative expression of genes.