Two segregating generations (F<sub>3</sub> and F<sub>4</sub>) from 6 × 6 half-diallel crosses, excluding reciprocals, of a sesame breeding program were exposed to natural infection by the root rot pathogen (<i>Macrophomina phaseolina</i>) in two successive seasons (2004 and 2005). There was highly significant variability in the progeny of all investigated crosses which might be a valuable tool for further breeding programs for root rot disease management. The level of infection in 2004 ranged from 2.63% (cross P<sub>2</sub> × P<sub>5</sub>) to 52.42% (P<sub>4</sub> × P<sub>5</sub>) in the F<sub>3</sub>, and from 1.28% (P<sub>1</sub> × P<sub>5</sub>) to 51.78% (P<sub>4</sub> × P<sub>5</sub>) in the F<sub>4</sub>. During 2005, infection varied from 1.01% (P<sub>2</sub> × P<sub>5</sub>) to 50.91% (P<sub>4</sub> × P<sub>5</sub>) in the F<sub>3</sub>, and from 1.00% (P<sub>3</sub> × P<sub>4</sub>) to 48.00% (P<sub>4</sub> × P<sub>5</sub>) in the F<sub>4</sub>. These crosses were ranked resistant or highly susceptible and gave seed yields per feddan (= 4200 m) of 536.67, 361.67, 641.67, and 408.33, respectively. The F<sub>3</sub>’s and F<sub>4</sub>’s of five crosses, i.e. P<sub>1</sub> × P<sub>2</sub>, P<sub>1</sub> × P<sub>4</sub>, P<sub>1</sub> × P<sub>5</sub>, P<sub>2</sub> × P<sub>6</sub>, and P<sub>3</sub> × P<sub>4</sub>, were resistant in both segregating generations and both seasons. Such crosses might be helpful for breeding programs due to their stable resistance. Lines from the crosses P<sub>1</sub> × P<sub>6</sub>, P<sub>2</sub> × P<sub>4</sub> and P<sub>4</sub> × P<sub>5</sub> could also be used for improving resistance due to an increase of inherited resistance from one generation to another. The estimated heritability showed high values in all cases and indicated that selection for these traits could be useful for breeding programs for resistance to root rot with seed yield potential. Correlation coefficients showed that there were some positive correlations such as percentage of infection by <i>M. phaseolina</i> between both generations (F<sub>3</sub>’s and F<sub>4</sub>’s) as well as within each generation during a season’s evaluation, i.e. 0.742, 0.976, 0.846, 0.732, and 0.987. The highest significant and positive correlations assisted in the selection of some crosses to be used in breeding programs and will aid breeders to achieve sesame cultivars with charcoal root rot resistance.