The genus Calanthe includes species of terrestrial orchids that produce attractive flowers with diverse floral traits. Breeding programs have been established to improve the horticultural value of various Calanthe species, but studies to identify the genetic components contributing to the key phenotypic characteristics have not been undertaken. To understand the molecular mechanisms underlying floral development associated with floral morphology, color, and fragrance production, the flower buds of two typical Korean Calanthe species, C. discolor and C. sieboldii, were subjected to gene expression analysis by differential display RT-PCR (DDRT-PCR). A total of 66 non-redundant differentially expressed genes (DEGs) were isolated and sequenced. Of these, 26 and 40 DEGs were found to be highly expressed in C. discolor and C. sieboldii, respectively. Moreover, the expression patterns of a subset of genes presumably implicated in signal transduction, metabolic pathways, and hormonal signaling differed between the two species. The data presented here may improve our understanding of the mechanisms underlying floral development and contribute to advances in orchid biotechnology.