Abstract: The objective of this study was to compare some aspects of root anatomy of rice cultivars under irrigation and submerged conditions. Seedling of three new rice cultivars (Zayande-Rood, 829 and 216) were transferred to 9 lysiometers (200x120x100 cm) according to a randomized block design with two treatments (submerged and aerated condition) in three replicates. The amount of water consumption was recorded during growing season. Cross-sections of plant roots were obtained at two different times; two and four months after seedling. The root samples were prepared from 20 mm of tip. Root cross-sections were successively stained with 1% aqueous solutions of Methyl green and Congo red. Figures of sections were made by LM. Anatomical differences were observed among the three cultivars submitted to water regimes regarding the amount of aerenchyma tissue and cell walls of secondary tissues. The irrigated roots of the three cultivars presented a decreasing tendency in the proportion of the area of the cortex destined for the aerenchyma besides thickening of the cell walls of endodermis, pith and sclerenchyma layer cells. The rate of aerenchyma disappearing in the irrigated plants suggested different behaviors in different cultivars. Zyande-Rood and 829 cultivars exhibited extensive aerenchyma disappearing when the plants was irrigated compared to others. The sclerenchyma layer cell walls in 2-month-old roots were higher in irrigated plants and also was higher in Zayande-Rood cultivar. The result of xylem vessels wall indicated that the thicknesses of xylem vessels under submerged and irrigated condition were 3.6 and 7.9 μ in Zyande-Rood cultivar respectively. The thicknesses of endoderm cell wall of the submerged roots ranged from 4.6 to 10.8 μ for Zyande-Rood cultivar in submerged and irrigated conditions respectively and were lower for other cultivars. The water consumptions were 43.04 and 82.5 cm in whole season for irrigated and submerged condition, respectively.