SEQ CHAPTER \h \r 1Flood damage ranked second only to the combined effect of heat and drought stress in terms of economic losses to U.S. agriculture during 1990–2004. Flooding can reduce soybean yield by 17 to 43% at the vegetative growth stage and by 50 to 56% at the reproductive stage. Flood-tolerant soybean varieties, therefore, would provide substantial benefit to soybean producers. To investigate the tolerance response of soybean root to flooding stress, we grew soybean plants of the flood- tolerant plant introduction PI408105A and the flood- susceptible genotype S99-2281 in rhizotron boxes (31.5 x 42.5 x 3.8 cm) made of acrylic peg board. The rhizotrons were filled with top soil and one soybean was planted per box. Flooding treatment was applied at the early vegetative stage (V2) by adding water to the rhizotron boxes up to 3 cm above the soil surface. Plants of the control treatment were not flooded. The acrylic pegs glued to the board at 2.5 cm apart preserved the root architecture for sampling and imaging when the soil was washed off. Root growth and death and adventitious root formation were quantified every three days during the two week flooding period using a digital camera and a WinRhizo scanner. Root porosity was determined by pycnometric and anatomical methods. The PI408105A plants produced three-fold more root length as the S99-2281 plants under the control treatment. Flooding reduced root growth in both genotypes but the tolerant genotype produced twice as much root length in the lowest 15 cm of the soil profile compared to the susceptible genotype. The ability of soybean plants to produce more roots at greater depths under flooding stress was associated with the formation of aerenchyma for transport of oxygen, which allows the PI 408105A plants to recover better after flooding stress.