The number of people suffering from chronic undernourishment in sub-Saharan Africa has increased. The potential of the cowpea to be the crop of the future to address food and nutrition insecurity is evident in sub-Saharan Africa. This study was carried out to evaluate cowpea accessions for early maturity and drought tolerant genotypes with potential for higher yields for smallholder farmers in South Sudan. One hundred and six cowpea accessions were sourced from different backgrounds. Their genetic diversity was assessed using both agromorphological traits and molecular approaches. Nine discriminatory clusters yielded cophenetic correlation coefficient values of 0.76. Results of molecular study revealed genetic divergence among the assembled cowpea panel creating an opportunity for population development through introgression of new alleles. The SNP markers used in this study could be utilized to analyse and group collections in the future. Forty-nine accessions selected from 106 genotypes were screened under well-watered and drought stressed conditions for selection of parental lines for population improvement using 7× 7 lattice square design. Five cowpea accessions from South Sudan and three from Burkina Faso, Niger and Nigeria were identified and selected for crosses. Hybridisation was carried out using hand emasculation and pollination. The North Carolina II mating design generated 15 F1 populations. The F1s were then backcrossed to the local parent to develop BC1F1. The 15 BC1F1 populations with their parents as checks were evaluated using an alpha lattice design to advance promising genotypes to the next …