Cowpea is an important drought-tolerant crop that is grown mainly in Africa. The objective of this study was to conduct association mapping of drought tolerance phenotype with seedling and yield-related traits in cowpeas. A total of 60 cowpea accessions were used in the study. Single-nucleotide polymorphisms (SNPs) were discovered through genotyping-by-sequencing (GBS). In the primary pipeline analysis, fragments of poor-quality sequences with reproducibility below 90% and read depths lower than 3.5 for SNPs or 5 for presence–absence markers were filtered out. Approximately 2.5 million sequences per barcode/sample were identified and used in marker calling. Association mapping was conducted using single-marker regression (SMR) in Q Gene, and the general linear model (GLM) and mixed linear model (MLM) built in TASSEL v5.0. The population of the cowpea accessions was analyzed using STRUCTURE 2.3.4. Inferred number of populations (∆K) of cowpea accessions grown in the greenhouse and glasshouse were six (6) and seven (7), respectively. Approximately 2.5 million sequences per barcode/sample were identified and used in marker calling. The total number of SNPs in the raw file was 438,198. After a quality control procedure, a variant call format (vcf). One SNP marker, was associated with number of pods (NP) with a p value < 0.001 while fifty SNP markers, were associated with pod weight (PWT) at p < 0.001. The same number of four SNP markers, were associated with average seeds per pod (AVSPD) at p < 0.001 and also with pod length (PL). Five SNP markers, were associated with pod width (PWDTH) at p < 0.001. Major differences among the significantly associated SNPs were observed in the two environments which were under different temperature conditions. The 65 SNP markers identified can be used in cowpea molecular breeding to select for drought tolerant phenotypes in cowpea through marker assisted selection (MAS)