Background <p>Information on the genetic variation and phylogenetic relationships of white lupin (<i>Lupinus albus</i> L.) can support the increasing plant breeding effort on this crop. This study aimed to: (a) assess the genetic variation relative to germplasm type (landrace, modern cultivar or wild type), landrace region of origin, landrace accession within region, and genotype within landrace accession; (b) explore landrace phylogenetic relationships; and (c) assess the consistency between molecular and morphophysiological diversity.</p> Results <p>A landrace collection of 112 accessions classified into 11 regional pools and a set of modern cultivars underwent genotyping-by-sequencing characterization (genotyping four plants per landrace) and evaluation of 11 morphophysiological traits. Molecular data of four wild-type accessions were added. Multi-dimensional scaling indicated a sharp genetic distinctness of wild-type material and a fairly modest diversity of modern cultivars relative to landraces. Mantel’s test revealed low consistency between molecular and morphophysiological diversity. Overall, landrace germplasm exhibited high genetic differentiation. The size of variance components in an analysis of molecular variance ranked as: genotype within landrace &gt; landrace within regional pool &gt; regional pool. Cluster analysis, nucleotide diversity, number of private alleles, phylogeny and migration analyses suggested a dual or divergent crop domestication in Greece and Italy, followed by migration of Greek germplasm into North-Eastern Africa and the Near East, extensive migration of Italian germplasm in the Mediterranean basin, and hybridization of the two genetic pools in various regions.</p> Conclusions <p>Our results increase our knowledge of white lupin diversity and phylogeny and can help optimize the exploitation of genetic resources.</p>