Formosan lily (Lilium formosanum), a species endemic in Taiwan, is characterized by showy and fragrant flowers. To understand the gene expression at its reproductive phase, we constructed a suppression subtractive cDNA library of immature flower buds, from which 1,324 expressed sequence tags (ESTs) were randomly selected and sequenced. These EST sequences were clustered into 974 nonredundant sequences. Based on BLAST searching, functions of 376 sequences (39%) were determined, and 80 sequences showed high similarities to genes encoding hypothetical proteins without known functions. Another 518 sequences did not show significant homology to any known sequences and were therefore classified as novel sequences. Further analyses of the 376 ESTs sequences revealed high abundance of stress-related and flower-development genes. The highly expressing stress-related transcripts include 39 with high similarities to lipid transfer proteins, five to ascorbate peroxidases, and five to heat shock proteins 70. Using real-time quantitative RT-PCR analysis, we further revealed the expression of these three genes in the immature flower buds and in the pistils or stamens of the blooming flower of Formosan lily collected from alpine regions. These results suggest that the flower of L. formosanum possesses a significantly elevated level of stress genes in response to alpine environment and the ESTs analyzed here represent a valuable resource for studying a resistance mechanism of the reproductive organs of Formosan lily.