Recent changes in climate have led to very dramatic temperature fluctuations in winter and spring. Warmer winters and early springs and sudden temperature dips to subzero in mid to late spring are of common occurrence in the United States of America. Horticultural plants, including spring blooming ornamental species, fruit trees, and vegetables are very vulnerable to such weather conditions. This study was performed to identify genes conferring tolerance to the freeze-thaw stress in flower buds of Helleborus orientalis, using genome wide mRNA profiling (cDNA differential display) and quantitative real-time polymerase chain reaction analysis. Flowers were collected from field plants at frozen-defrosted-recovery stages and an incubator experiment was conducted under a corresponding temperature regime (0-4-10 ± 1°C). Based on expression patterns and putative functions of the isolated genes, programmed cell death, water transportation (aquaporin proteins), and oxidative phosphorylation are proposed to play key roles in the tolerance mechanism for freezing temperature; genes in the biosynthesis of steroids and terpenes were activated as soon as the temperature warmed up to above freezing point. This study provides novel understanding and gene sequences to be used for improving tolerance to subzero freezing temperature in floral plants.