White lupin (Lupinus albus L.) is a pulse whose 49 domestication started about 3000 - 4000 years ago in the Mediterranean region [1]. It is cultivated for its seeds that contain high levels of proteins and are used both for food and feed [2]. The wild forms of the species can only be found in the Balkan region and evidence of its earliest use as a green manure and grain crop come from that same region [3]. Early Greek farmers selected larger seeds and white flowers, and presumably soft seededness (water permeable seeds) was the earliest domestication trait. Greek and Roman literature suggests that seed indehiscence (i.e. resistance to pod shattering) had not yet been incorporated by the first century A.D. [4]. Wild collections and landraces of white lupin contain high levels of quinolizidine alkaloids that accumulate in the seed, resulting in a bitter taste and possible toxicity. Lysine-derived alkaloids are characteristic of the Genistoids [5–7], a monophyletic basal clade belonging to the Fabaceae family. Traditionally these bitter compounds are removed from white lupin seeds by soaking in water, a practice that is still carried out today across the Mediterranean and Nile regions [1]. However, this is uneconomic on a broad-scale, which motivated the identification of low alkaloid mutants in Germany in the 1930s, aided by advances in chemistry [4]. Modern cultivars of white lupin incorporate low alkaloid genes, hence the term ‘sweet’ lupins. Breeding efforts have rarely been intensive or sustained over long periods. As a result, white lupin yields remain low and highly variable, in comparison to similar pulses like soybean for which important breeding efforts have been made internationally. Although white lupin cultivation represents a promising crop for Europe, in a political context aiming towards plant protein independence, the lack of well characterised genetic resources has been hampering a fast deployment of white lupin as an alternative crop to soybean imports. The recent sequencing of white lupin genome [8,9] demonstrated a resurgence of interest for this 74 “old” crop. We believe that white lupin intragenomic diversity might reflect the early traces of its slow and sporadic domestication history. Here we report a pangenome for white lupin that reveals important aspects of the species diversity, single nucleotide polymorphisms (SNPs) and gene presence– absence variations (PAVs). We construct a species pangenome consisting of ‘core’ genes that are present in all individuals and ‘variable’ (soft-core or shell) genes that are absent in some individuals [10,11]. Building on this comprehensive dataset, we were able to identify a deletion in the QTL region associated with late flowering in Ethiopian white lupins. The deleted gene is a homolog of the FT (Flowering Time) gene, suggesting that this deletion is at the origin of the need for vernalization in these accessions. Our analyses provide new perspectives on white lupin intra species diversity and domestication history.