By this study, thirty rice varieties were evaluated for anaerobic flooding tolerance using the direct sowing method. Phenolic profiles of strong and weak tolerant varieties were identified and compared based on HPLC chromatograms. The germination rates and shoot heights of rice were recorded for calculating the seedling vigor, which indicate the tolerant ability of rice in flooding condition. The results revealed a high variation of germination rate (10.01 to 100%), shoot height (0.35 to 78.17 mm) and seedling vigor (0.05 to 72.83). There was a high correlation between (r = 0.71) germination rate in 5 cm and 10 cm flood. Phenolic and flavonoid contents of the strong tolerant cultivar significantly and proportionally increased in the flooding levels (5 cm and 10 cm). There was a total difference in terms of number of phenolic acids found in the strong and weak tolerant varieties. In particular, six phenolic acids (gallic acid, catechol, caffeic acid, syringic acid, vanillin, and ellagic acid) were only identified with high concentration in the strong tolerant cultivar. The findings suggest that the phenolics presented in the strong tolerant varieties probably have a certain function in response and adaptation to anaerobic flooding condition. Further researches on exogenous application of these phenolic acids to increase the flooding tolerant level of rice should be continued at both green house and field treatments.