We evaluated the effects of the soil temperature (15, 25 and 35°C) and soil anoxia from flooding for 20 days on citrus rootstock seedlings of CT33 trifoliate, Carrizo citrange and Troyer citrange along with Tucuman, Pomeroy and Rubidoux trifoliates in a greenhouse. Flooding had no effect on shoot water potential (Psi s) at 25°C but at 15°C and 35°C, there were differences from non-flooded trees. Carrizo and Troyer had higher Psi s than CT33, and Tucuman had the highest Psi s among the trifoliates. Soil temperature was more important than flooding in determining plant water relations. At 35°C, ACO 2 was reduced up to 14% of non-flooded plants in 4 days, particularly in CT33. In flooded seedlings, across the three genotypes, the decrease of F v/F m was highest at 35°C. Troyer rootstock maintained lower ACO 2 at 35°C Based on leaf net gas exchange, chlorophyll fluorescence and water relations, above optimal soil temperature accelerates seedling deterioration. CT33 was less tolerant than Carrizo and Troyer at 35°C, whereas Tucuman, Pomeroy and Rubidoux had similar tolerance to anoxia regardless of soil temperature.