In inundation areas in rainfed lowland and inland valleys of Guinea as well as other regions in Africa, submergence for a few days to a few weeks with a water depth less than 50 cm occurs in rice cultivation during the rainy season. Young rice seedlings after transplanting are particularly vulnerable to submergence stress. Oryza glaberrima Steud. is well adapted to growth in inundation areas with deepwater conditions in West Africa; however, it is not evident whether it resists short-term submergence stress after transplanting. The purpose of the study was to understand the physiological responses of rice plants after transplanting to short-term submergence stress under rainfed conditions for O. glaberrima by comparison with several genotypes of Oryza sativa L. from Guinea. Eight genotypes of O. glaberrima and seven genotypes of O. sativa including two shoot elongation genotypes, one submergence tolerant genotype as a control cultivars, and four genotypes of common cultivars in West Africa were used. Thirty day-old seedlings were submerged completely for 10 days with medium deepwater conditions at 45 cm water depth at 13 days after transplanting in a lowland field. O. glaberrima showed higher shoot elongation ability during submergence than any genotype of O. sativa that we tested. However, O. glaberrima lodged easily after desubmergence due to longer and rapid shoot elongation during submergence, and thus triggered a decrease in its survival rate. The submergence tolerant genotype of O. sativa maintained the dry matter weight of the leaf blade during submergence through the inhibition of shoot elongation. We suggest that O. glaberrima is susceptible to short-term submergence while it may adapt to prolonged flooding because of improved restoration of aerial photosynthesis and survival rate through shoot elongation ability.