Cowpea is a major source of vegetable protein but its production is constrained by drought resulting in yield loss. Developing drought tolerance varieties can enhance yield and reduce the need for supplemental irrigation. Breeding for drought tolerance requires the knowledge of its genetic basis. Genetic basis for some seedling traits in cowpea was investigated. Seven generations (P1, P2, F1, RF1, F2, BC1 and BC2) each derived from two crosses involving two highly drought tolerant (Danilla and IT97K-499-35) and one highly susceptible parents (Tvu7778) were evaluated for drought tolerance in the screen house. Data on Seedling height (SH), Seedling terminal leaflet area (SLA), Seedling Vigour (SV) and Recovery Capacity (RC) were collected. The SV was assessed on a scale of 1 (highly-tolerant) – 9 (highly-susceptible), while RC (%) was evaluated at 5 d interval for 30 d. The hybrids F1 and RF1 showed the best performances in both crosses with SV ranged from 2.50 ± 0.00 in Danilla × IT97K-499-35 cross to 6.50 ± 1.00 in the Danilla × TVU7778 cross. In both crosses, F1 and RF1 had 100.0% RC. Both dominance (46.5–68.6%) and additive (31.4–53.5%) effects were found similar and important in all the traits under water stressed. The six-parameter model indicated few cases of gene interactions, mostly dominance × dominance. Narrow sense heritability ranged from 33.5% for SH to 50.1% for SLA in the cross Danilla × TVU7778 at terminal water stress. Inheritance of these traits in cowpea involved both additive and dominance gene action. However, dominance and/or dominance × dominance effects had a more pronounced effect in genetic control of all characters.