Alternate wetting and drying (AWD) is one of the key water-saving cultivation technologies for rice, which has been shown to effectively increase water use efficiency while it still sometimes suffers from yield penalty. In AWD, soil moisture inherently fluctuates between wet and dry, which may stressfully affect plant growth. We previously reported that an upland rice variety, IRAT 109 showed higher yield than a lowland rice variety, Taichung 65 in AWD (Kakehashi et al., 2015), and then assumed that root functions may be involved in such genotypic variation in yield under AWD. This study therefore aimed to identify root traits that contribute to the adaptation to AWD. We grew IRAT 109, Nipponbare (NIP) and Taichung 65 (T65) under continuously waterlogging (CWL, soil water potential (SWP) ≒ 0 kPa), AWD (SWP fluctuated between 0 and -38 kPa) and continuously drought (CD, SWP ≒ -36 kPa), and determined root respiration rate, hydraulic conductance of the whole root system (Lp), osmotic hydraulic conductivity (Lpr (os)) in which water flow is driven by osmotic potential gradient, hydrostatic hydraulic conductivity (Lpr (hy)) in which water flow is driven by hydrostatic pressure, and their related traits. Results revealed that IRAT 109 increased root respiration rate and Lpr (os) after rewatering after drought in AWD. Furthermore, Lp and Lpr (hy) in AWD decreased in T65, while were maintained in NIP and IRAT 109. Lpr (os) / Lpr (hy) ratio of all the varieties in AWD increased as compared to CWL and those of IRAT 109 and NIP in AWD were higher than that of T65. These results indicate that IRAT 109 enhanced active water transport through cell-to-cell pathway and kept high Lp especially after rewetering in AWD. Future study is needed to determine if these root responses would contribute to the growth of IRAT 109 in AWD.