We analyzed several genes that were strongly expressed in response to dehydration of almond (Prunus amygdalus (L.) Batsch) as a means of identifying and determining the genetic basis of mechanisms involved in drought tolerance. The advantages of using almond as a model system for studying dehydration tolerance in woody species include its small diploid genome and its adaptation to drought. We used the differential expression technique cDNA-AFLP (amplified restriction fragment polymorphism derived technique for RNA fingerprinting) to identify transcripts that accumulated in mature embryos and in in-vitro-cultured plantlets subjected to desiccation or abscisic acid (ABA) treatment. The reverse northern approach was used to differentiate between true differential bands and false positives. Some of the predicted polypeptides exhibited similarity to published protein sequences, including a transporter of nitrogenous compounds, a 1-acyl-sn-glycerol-3-phosphate acyl transferase, a low molecular weight heat shock protein, a cysteine proteinase and a constitutively expressed proline-rich protein. We also compared the levels of expression of the identified genes in leaves of young trees of eight almond cultivars differing in drought tolerance.