Sorghum genetic diversity features morphological races such as Bicolor, Caudatum, Durra, Kafir and Guinea, as well as geographical origins throughout Africa and Asia. Among the different genetic groups, the Guinea margaritiferum subrace receives a particular status suggesting a secondary domestication event. Whole genome sequencing data provide new ground to better understand sorghum genetic diversity. We have access to the wealth of sequencing data produced by the Sorghum Genomics Toolbox (SGT) project. We have complemented the SGT sample with 37 accessions that have extended the coverage of the margaritiferum subrace. After a new SNP call, we recovered a dataset of 972, mostly cultivated, accessions characterised with 31 million SNP loci. We performed principal component analyses (PCAs) after applying different thresholds for minimum allele frequency and for missing data. Overall, we obtained high-level components that differentiate Guinea margaritiferum materials, confirming the special status of this subrace. On this basis, we are characterising the distribution of this differentiation along the genome and the extent of genetic exchange between the margaritiferum subrace and the other cultivated forms. The data is ready to be accessed on our South Green platform using the Gigwa data management tool and various analytical options that will make it an excellent resource for data mining by researchers and students interested in germplasm management and improvement.