This study was aimed at investigating genomic variation in wild cowpea populations to understand its implications for crop improvement. The method adopted in the study encompassed population structure analysis and gene flow studies, supported by statistical tools, to elucidate genetic dynamics from 3 wild cowpea varieties grown on a complete randomized block design with 3 replicates. Results indicate distinct phenotypic traits and genomic markers associated with adaptive mechanisms, with significant variability observed across populations. Genomic analyses revealed diverse variations across chromosomes and loci, highlighting the rich genetic landscape of the wild cowpea populations. Notably, gene flow analysis demonstrated dynamic genetic exchange between wild and cultivated populations, influencing genetic diversity. The study provides insights into genotype-phenotype associations and provides useful implications for crop breeding. The findings highlighted the importance of conserving wild cowpea populations and developing genetic diversity for sustainable agriculture. In conclusion, the findings of this are useful in deciphering the interactions between the various factors in genotype phenotype correlations and thus helpful in crop improvement projects, stressing that wild cowpea populations and the genetic resource for sustainable agriculture should be conserved and evolved.