The genetic diversity in 48 lupin (Lupinus albus (L.) accessions collected from the Amhara region, Ethiopia, was assessed using seed storage protein markers (SDS-PAGE). A total of 30 different protein bands with sizes ranging from 11 to 100 kDa were detected. The average number of protein bands, the percentage of polymorphism, and gene diversity in the accessions were 16.96, 20.35, and 0.072, respectively. Genetic diversity estimates showed that West Gojam and Bahir Dar areas could be the most important sources for lupin genetic resources. The pair-wise comparison of genetic distances (GDs) among the accessions ranged from 0.011 to 0.378. The most distantly related accessions were accession 6, collected from the West Gojam zone, and accession 28 from the Bahir Dar area. Principal coordinate analysis (PCoA) showed the absence of a distinct group, and most of the accessions were intermixed. Population structure analysis revealed that the 48 lupin accessions could be assigned to three clusters. Similar to PCoA, no defined grouping based on geographic origin was observed. Accessions from different geographic origins being grouped together could be attributed to a common origin for the various accessions in the different zones, or it could be the result of seed-mediated gene flow among different lupin growing areas of the country.