Seed production is a major component of the commercial development of a variety but breeding for seed yield is expensive. A set of 400 cultivated lucerne accessions were phenotyped for seed yield traits in two locations and genotyped with GBS markers. A large diversity was found among accessions but the heritability of the traits was moderate. QTL were found for one seed yield component. Genomic prediction was moderate to high, depending on the traits and the locations. Molecular breeding could be effective to assist lucerne selection for seed yield, in addition to forage-related traits.