AbstractOne of the most important screening techniques used in cowpea selection for drought tolerance is screening at the seedling stage. The objective of this study was to phenotype 60 cowpea genotypes for seedling drought tolerance in screen houses (glasshouse and greenhouse). A triplicated 6 × 10 alpha lattice design with four blocks was used for the experiments. After planting, pots were watered to field capacity, thereafter watering was completely withheld for 4 weeks after planting (WAP), when plants were at the three-leaf stage. Principal component analysis revealed that of the 14 variables, the first four expressed more than 1 eigenvalue. Data showed that PC1, PC2, and PC3 contributed 39.3%, 15.2%, and 10% respectively, with 64.68% total variation. Bartlett’s test of sphericity was significant at p<0.05, while the Kaiser-Meyer-Olkin measure of sampling adequacy was 77. A PCA plot and biplot showed that the number of pods (NP), seeds per pod (SP), survival count (SC), pod weight (PWT), and stem wilting in week one (WWK1) had the most significant contributions to genetic variability to drought tolerance and to yield after stress imposition Based on the PCA, biplot, and cluster plot, the accessions IT 07-292-10, IT 07-274-2-9, IT90K-59, 835-911, RV 343, and IT 95K-2017-15 had the maximum variability in terms of number of pods, seeds per pod, survival count, pod weight and wilting in week one after drought imposition. Cowpea accessions 835-911, IT 07-292-10, RV 344, Kangorongondo, and IT 90K-59 were the major individuals that contributed mainly to domain information model (DIM) 1 and 2. The accessions that contributed the least were IT 89KD288, Chibundi mavara, and TVU12746. Thirty-six cowpea accessions from both screen houses were tolerant to drought, 15 were moderately tolerant, while 23 were susceptible. The findings of the study provided a useful tool for screening and determining drought-tolerant and susceptible accessions at the seedling stage. Thirty-six cowpea accessions from both screen houses were tolerant to drought as well as those that showed great variability can be used as parents in future cowpea breeding programmes.