The genetics of yardlong bean (Vigna unguiculata ssp. unguiculata cv.-gr. sesquipedalis), a vegetable form of cowpea, is of particular interest because the genome of this legume has experienced divergent domestication. Kongjaimun et al. develop two genetic linkage maps and QTL analysis for 24 domestication-related traits and find that the QTLs show co-location on several narrow genomic regions on almost all linkage groups. Comparison with other domesticated species reveals similarities with azuki bean (V. angularis) but differences with rice bean (V. umbellata), and some genomic regions for seed and pod size are conserved. The results provide a foundation for marker-assisted selection of domestication-related QTLs in yardlong bean and enhance our understanding of domestication in the genus Vigna.