Under drought stress, adventitious roots of Alternanthera philoxeroides seedlings will grow long thick fleshy roots, which are assumed to improve performance of the plant by more efficient reservation and absorption of water from deep soil layers. In this study, the differential display technique was used to clone morphogenesis-related genes from A. philoxeroides roots treated with drought, which would help to improve crop plants' drought-tolerance by transgenic method; by 15 pairs of primer combinations, twenty putative drought up-regulated gene segments induced by drought were obtained; and one of them was confirmed by reverse northern blot, and subsequently cloned and sequenced. A homologous analysis revealed that it might be a new sequence. Semi-quantitative RT-PCR analysis showed that the gene was up-regulated by drought and salt stress.