Inheritance of submergence tolerance in lowland rice varieties were evaluated for score of tolerance in main stem and total plants of 8 rice varieties (FR13A, Chenab64-117, BKNFR76106-16-0-1-0, IR8234-OT-9-2, NSG 19, RD 7, KDML 105 and IR 42) and their F(,1) 28 crosses obtained from diallel cross. Additive and nonadditive variance showed highly significant in both main stem and total plants. Narrow sense heritability of 0.6713 and 0.7255 in main stem and total plants showed important of additive gene effects. The significant of general combining ability effects were presented in FR13A and Chenab64-117 in both main stem and total plants while IR8234-OT-9-2 was significant in main stem. The crosses which contained highly specific combining ability effect in main stem and total plants were BKNFR76106-16-0-1-0/FR13A and RD 7/Chenab64-117 while IR 42/Chenab64-117 and IR 42/RD 7 showed only in main stem. The dominant gene actions were partial dominance in both main stem and total plants and non allelic interaction appeared in main stem. The high general combining ability effect varieties FR13A contained mostly dominant genes while Chenab64-117 was recessive genes. The tolerance of total plants were positive correlated with main stem in linear regression (tolerance of total plants = 3.18 + 0.666 of main stem).