The molecular basis of many physiological and/or phenotypic adaptations of alpine plants remains largely unknown. The upper leaves of what are termed "glasshouse plants" have been transformed into translucent bracts that cover their inflorescences. This change in appearance is believed to allow such plants to maintain normal sexual reproduction under very cold conditions. Thus, it is hypothesized that the foliar roles of these bracts have been altered as an adaptation to alpine environments. In the present study, a test of this hypothesis revealed distinct physiological and anatomical differences (especially related to photosynthesis) between the bracts and normal leaves in one 'glasshouse' species, Rheum nobile Hook. f. and Thomson. A cDNA-AFLP analysis, was conducted to identify candidate genes involving differential expression in bracts and normal leaves, detected 323 (5.4%) transcript-derived fragments (TDFs) that were differentially expressed (up- or down-regulated) among 6,000 TDFs recovered. In total, 110 differentially expressed TDFs were sequenced, of which 52 were homologous to genes reported from other plants. More than half of the candidate genes represented by the unidentified TDFs may be specific to the Rheum lineage or have arisen through adaptive processes in alpine plants. All putative genes involved in photosynthesis had been down-regulated, while those related to stress and defense response were up-regulated in the bracts. These differentially expressed genes are highly congruent with physiological and anatomical differences between the bracts and normal leaves, indicating that they are associated with functions that confer a physiological advantage in alpine conditions.