Alternanthera philoxeroides is one of the rather few amphibious plants that can normally grow in both water and upland conditions. Adventitious roots of Alternanthera philoxeroides seedlings will grow long, thick, fleshy during drought stress, which are assumed to improve performance of the plant by more efficient storage and extraction of water from deep soil layers. In order to isolate cDNA clones of morphogenesis-related genes from A. philoxeroides roots, the seedlings were treated with drought and the differential display technique was used. By using 18 primer combinations, nineteen putative drought up-regulated gene segments were obtained and one of them was confirmed having been up-regulated by reverse northern blot and subsequently cloned and sequenced. A homologous analysis revealed that it might be a new gene segment. Semi-quantitative RT-PCR analysis showed that the gene was up-regulated by drought and salt stress.