The internodes of deepwater rice can elongate in response to rises in water level. This unique character allows deepwater rice to survive severe flooding during the monsoon season in South and Southeast Asia. Our previous quantitative trait locus (QTL) analysis of a deepwater rice cultivar (Oryza saliva) detected QTLs on chromosomes 1, 3 and 12. In this study, we produced three nearly isogenic lines (NILs) possessing each of the three QTLs by backcross introduction of each chromosomal region into a non-deepwater rice cultivar. The NILs showed internode elongation under deepwater conditions, and we were able to demonstrate the existence of the QTLs and to evaluate the effect of each QTL. Using progenies of the NILs, we mapped all QTLs between molecular markers. Comparison of the location of the most effective QTL between the rice cultivar (O. saliva) and a wild rice species (O. rufipogon) indicated that the QTL on chromosome 12 is common and is the most important QTL for internode elongation in deepwater condition.