The Balkan endemic plant species Haberlea rhodopensis belongs to the group of resurrection plants. The members of this small group of angiosperms tolerate extreme dehydration of their vegetative tissues, which are able to recover very rapidly upon rehydration. In this respect, resurrection plants are a unique model intensively studied to reveal the secrets of desiccation tolerance. To date, the knowledge on the molecular biology of H. rhodopensis is very limited. Here, we report on the application of a cDNAAFLP analysis to examine gene expression in leaves of Haberlea during dehydration. Twenty transcripts among 33 sequenced cDNA fragments appear to be involved in energy metabolism, transport, cell-wall biogenesis, signal transduction, or are probably transcription regulators according to their putative function. Expression patterns of two up-regulated (HrhDR8, HrhDR35) and two down-regulated (HrhDR6, HrhDR25) transcripts were verified by sqRTPCR analysis at different stages of water stress. The results demonstrated that two up-regulated transcripts HrhDR8 and HrhDR35 encoding putative succinate-dehydrogenase and xyloglucan endotransglucosylase/hydrolase (XTH), respectively, were induced during early stage of dehydration, persist in desiccated state, and subsequent rehydration of Haberlea. Their possible involvement in drought tolerance is discussed.