Alligator weed, Alternanthera philoxeroides (Mart.) Grisb, is an amphibious plant with long thick fleshy roots that develop from adventitious roots under drought conditions. To clone differentially-expressed genes from the roots of A. philoxeroides we applied both mRNA differential display and rapid amplification of cDNA ends techniques. A cryptogein-like gene of A. philoxeroides, designated as ApCL, was cloned. On the basis of semi-quantitative RT-PCR analysis results, we demonstrated that the ApCL gene was upregulated under drought and salt stress conditions. After ApCL was transferred to Pichia pastoris GS115 and its resistance to drought and salt then increased by >100 %. Therefore, the ApCL gene of A. philoxeroides was likely involved in drought and salt tolerance responses.