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Caragana is a native desert shrub with high forage values and stress tolerance, as well as sand-fixing capabilities. Some Caragana species, including C. korshinskii, C. microphylla, and C. intermedia, are commonly used for vegetation restoration programs in the Loess Plateau region of northwestern China and are known to have ecological benefits and high commercial value. In this study, full-length sequences of Cu/Zn-SOD genes were isolated from three Caragana species using degenerate polymerase chain reaction (PCR) and rapid amplification of cDNA ends (RACE) techniques, and their expression under drought stress conditions were investigated. The cloned SOD cDNAs contained a predicted open reading frame (ORF) of 459 bp encoding a polypeptide of 152 amino acids with a theoretical molecular weight of 15.2 kD. Cu/Zn-SOD cDNA of C. korshinskii and C. intermedia shared 100% sequence identity, implying a close relationship. A 24-bp specific sequence was found in the 3-UTR region of C. microphylla Cu/Zn-SOD cDNA, and reverse transcription RT-PCR and genomic PCR confirmed the feasibility of the 24-bp sequence as a DNA marker for rapid variety identification of C. microphylla. RT-PCR revealed that the expression of the Caragana Cu/Zn SOD genes was induced by PEG-simulated drought stress and ABA. The three Caragana Cu/Zn-SOD genes showed similar expression patterns, and no significant differences in transcriptional level were observed among the three genes. These results increase our understanding of the molecular mechanism of drought tolerance and can be used to improve vegetation restoration programs of Caragana plants.