to acquire final version. While analyses based on the genotypic SNP data only supported the division of the included populations into three main groups, Khoe-San, Bantu-speakers and nonAfrican populations, haplotype analyses revealed finer structure within Khoe-San populations. Through using only 44 short SNP haplotypes (compiled from a total of 220 SNPs), most of the Khoe-San groups could be resolved as separate groups by applying STRUCTURE analyses. Therefore, by carefully selecting a few SNPs and combining them into haplotypes, we were able to achieve the same level of population distinction as achieved previously in high-density SNP studies on the same population groups. Using haplotypes proved to be a very efficient and cost-effective way to study population structure.