Parallel evolution provides an excellent framework to infer the genetic bases of adaptive traits and understand the importance of natural selection in shaping current biodiversity. The upper leaves of the “glasshouse plants” transform into translucent bracts that show numerous adaptions in alpine habitats. It remains unknown whether similar molecular changes occur under the parallel bract evolution of different “glasshouse” species. In this study, we compared the results on phenotypic and physiological differences and presented the results of cDNA-AFLP analyses of transcriptional changes between translucent bracts and normal leaves in Rheum alexandrae. We also examined the homologous candidate genes with the same expression changes between this species and another “glasshouse” species, R. nobile. We found that bracts of R. alexandrae are similar to those of R. nobile in anatomical features: chloroplasts have degenerated and chlorophyll contents are greatly reduced, which suggests that foliar photosynthetic functions in bracts of both species have been reduced or totally altered. Among the 6000 transcript-derived fragments (TDFs) in bracts and leaves of R. alexandrae, 420 (7%) were differentially expressed (up- or downregulated) between bracts and normal leaves. There were a total of 13 homologous TDFs with the same expression changes between R. alexandrae and the previously studied R. nobile. Except for the two that were not functionally annotated, eight of the homologous TDFs were found to be involved in stress and defense responses whereas the other three were related to photosynthesis. The up- or downregulation of these candidate genes was highly congruent with anatomical characteristics and adaptive functions of the bracts found for “glasshouse” plants. These findings suggested that the “glasshouse” phenotypes may have common molecular bases underlying their parallel evolution of similar adaptive functions and highlighted the importance of the natural selection in producing such phenotypes.