Abstract: With high ornamental and research value, Paphiopedilum micranthum is a species of the genus Paphiopedilum native to China, which is endangered and protected intensively by the country. However, there are few reports on its floral development mechanism because of the supply shortage and backward cultivation technology. In this study, a suppression subtractive hybridization (SSH) library was constructed using the cDNAs from the floral and vegetative buds of P. micranthum as the tester and the driver, respectively. The insert fragments were tested by PCR, and 288 clones with 500bp or longer from the library were selected for sequencing. Totally, 18 ESTs were obtained, after vector sequences removed and clustered. The ESTs were functionally annotated by Blast. Those which matched significantly with Nr database were further classified into functional groups including photosynthesis, biosynthetic metabolism, gene regulation, etc. Among them, a few sequences with homology to transposons or retro-transposons were obtained. The genes differentially expressed in floral buds of P. micranthum isolated in this study could make a base for investigating the molecular mechanism of floral development.