Several genes of model and crop species that function in plant adaptation to acid soils have recently been characterized, but little is known about the molecular basis of the stress tolerance of woody plants. In the present study, using cell suspension cultures of Acacia mangium, a leguminous tree habituated to tropical acid soils, genes up-regulated in response to lowering the medium pH and addition of AlCl3 were screened by successive differential display and semiquantitative RT-PCRs, followed by full-length determination by RACE (rapid amplification of cDNA ends)-PCR. A total of 57 genes were shown to be induced by low-pH and/or aluminum stresses, and 44 full-length sequences were identified and cloned. They included genes of a multidrug and toxic compound extrusion transporter that secretes citrate ions to chelate aluminum, ATP-binding cassette transporters, a plasma membrane H+-ATPase, and a CYP94A, known in other plants to be responsive to low-pH and/or aluminum stresses. Genes that have not been recognized to be stress-responsive were also up-regulated by low-pH/aluminum treatments. Many of these genes were induced in the stressed A. mangium seedling roots. The cloned genes should provide the resources for the identification of the factors that play roles in the adaptation of A. mangium to acid soils.