The objectives of this study were, firstly, to evaluate the varietal differences in flooding tolerance; and secondly, to understand the mechanism of flooding tolerance based on physical properties of seed germination. Twenty varieties (strains) of soybean with different seed sizes were used as materials. The results were summarized as follows: 1. No significant effect of seed size on germination was found under normal soil moisture; while under flooded condition, there were negative correlation in both seed size vs. germination (R = -0.88**) and seed size vs. % of seedling stand (R = -0.77**). That implied smaller seeds were more tolerant to flooded soil than the larger seeds. 2. A negative correlation was existed between seed size and speed of germination under normal soil moisture condition as well as under flooded condition. 3. Germination abilities between smaller seeds (G2120) and larger seed (Kaoshiung 8) were compared under flooded soil condition. Smaller seeds showed higher germination rate (96.7%) than larger seeds (30%). Mean days of germination were delayed for 3 days and 6 days in smaller and larger seeds, respectively. Germination coefficient and speed of germination were decreased around 60% and 90% in smaller and larger seeds, respectively. Percentage of seedling stand were decreased to 77.6% and 11.1% in smaller and larger seeds, respectively. 4. Under flooded condition, larger seeds had more sever testa cracking, and higher percentage of cotyledonary cracking and seed coat loosening than smaller seeds. More leachates were also found from larger seeds than from smaller seeds. The properties described above might therefore be explained to result in the reduction of TTC reducing ability in larger seeds. It implied that the viability and germinating ability of larger seeds were therefore lower than smaller seeds. 5. When comparing the germination abilities of variety VS 205 with different seed sizes under flooding, the results showed that smaller seeds also had the higher germination percentage (32.1% of control) than medium seeds (26.7%), or large seed (6.3%). 6. The reason of the differences of flooding tolerance in the variety VS 205 with different seed sizes was similar to that between varities. The difference was correlated with the increase of the percentage of cracked teata and cotyledon, and alos, the increase of electrical conductivity as seed size was increased.