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Experiments in nutrient solution were conducted to investigate the exudation of organic acids (OAs) induced by phosphorus deficiency (–P) and/or aluminium toxicity (+Al) in two contrasting soybean genotypes as related to internal OA concentration and related enzyme activities. Baxi 10 (BX10), a known P-efficient soybean (Glycine max[L] Merr.) genotype, was shown to be more resistant to +Al than a P-inefficient genotype Bendi 2 (BD2), indicating the potential of selecting soybean cultivars with dual resistance to –P and +Al. The two contrasting genotypes were further characterized for root exudation and formation of oxalate, malate and citrate and their related enzyme activities in response to –P, +Al or both combined. –P significantly induced malate and oxalate exudation from both soybean genotypes, although the P-efficient BX10 tended to excrete much more oxalate than the P-inefficient BD2. The +Al treatment triggered citrate efflux from both genotypes, with BX10 having a much greater efflux rate than BD2. Interestingly, –P did not appear to induce citrate exudation, whereas +Al had no obvious effect on malate or oxalate exudation from the two genotypes. The exudation of OAs was generally diminished under the coupled stress of –P and +Al in comparison with either single stress, implying a possible antagonistic effect of the two stresses on OA exudation. Root malate content was negatively correlated with its exudation in BX10 but positively in BD2. A similar tendency was observed for oxalate content and exudation only with less magnitude. Determination of six related enzymes, phosphoenolpyruvate carboxylase (PEPC), phosphoenolpyruvate phosphatase (PEPP), malate enzyme (ME), isocitrate dehydrogenase (ICDH), malate dehydrogenase (MDH), and pyruvate kinase (PK), in the root tips showed that their activities were not significantly altered during the early stage of treatments (2 and 4 days) whereas at 14 days after stress imposition, the activities of PEPC, PEPP, ME and ICDH were generally enhanced for both genotypes. However, the activity of these enzymes did not appear to be correlated with OA exudation or formation. This study clearly demonstrates that OA exudation is differentially induced by –P and +Al in soybean plants, with specific induction of oxalate and malate by –P and citrate by +Al. The lack of a close relationship between OA exudation and internal concentration or enzyme activities may suggest that the regulation of OA formation and exudation by –P and/or +Al could be imposed at different stages.