SummaryVigna unguiculatais an important legume crop worldwide. The subsp.sesquipedalisandunguiculataare the two major types grown; the former is mainly grown in Asia to produce fresh pods, while the latter is mainly grown in Africa to produce seeds. Here, a chromosome‐scale genome for subsp.sesquipedaliswas generated by combining high‐fidelity (HiFi) long‐read sequencing with high‐throughput chromosome conformation capture (Hi‐C) technology. The genome size for all contigs and N50 were 594 and 18.5 Mb, respectively. The Hi‐C interaction map helped cluster 91% of the contigs into 11 chromosomes. Genome comparisons between subsp.sesquipedalisandunguiculatarevealed extensive genomic variations, and some variations resulted in gene loss. A germplasm panel with 315 accessions ofV. unguiculatawas resequenced, and a genomic variation map was constructed. Population structure and phylogenetic analyses suggested that subsp.sesquipedalisoriginated from subsp.unguiculata. Highly differentiated genomic regions were also identified, and a number of genes functionally enriched in adaptations were located in these regions. Two traits, pod length (PL) and pod width (PW), were observed for this germplasm, and genome‐wide association analysis of these traits was performed. The quantitative trait loci (QTLs) for these two traits were identified, and their candidate genes were uncovered. Interestingly, genomic regions of PL QTLs also showed strong signals of artificial selection. Taken together, the results of this study provide novel insights into the population differentiation and genetic basis of key agricultural traits inV. unguiculata.