Understanding the genetic structure and diversity of crops facilitates progress in plant breeding. A collection of 270 bambara groundnut (Vigna subterrenea L) landraces sourced from different geographical regions (Nigeria/Cameroon, West, Central, Southern and East Africa) and unknown origin (sourced from United Kingdom) was used to assess genetic diversity, relationship and population structure using DArT SNP markers. The major allele frequency ranged from 0.57 for unknown origin to 0.91 for West Africa region. The total gene diversity (0.482) and Shannon diversity index (0.787) was higher in West African accessions. The genetic distance between pairs of regions varied from 0.002 to 0.028 with higher similarity between Nigeria/Cameroon-West Africa accessions and East-Southern Africa accessions. The analysis of molecular variance (AMOVA) revealed 89% of genetic variation within population, 8% among regions and 3% among population. The genetic relatedness among the collections was evaluated using neighbor joining tree analysis, which grouped all the geographic regions into three major clusters. Three major subgroups of bambara groundnut were identified using the ADMIXTURE model program and confirmed by discriminant analysis of principal components (DAPC). These subgroups were West Africa, Nigeria/Cameroon and unknown origin that gave rise to sub-population one, and Central Africa was sub-population two, while Southern and East Africa were sub-population three. In general, the results of all the different analytical methods used in this study confirmed the existence of high level of diversity among the germplasm used in this study that might be utilized for future genetic improvement of bambara groundnut. The finding also provides new insight on the population structure of African bambara groundnut germplasm which will help in conservation strategy and management of the crop.