Abstract Population data regarding autosomal single nucleotide polymorphisms (SNPs) variation in African populations are very limited. The aim of this work was to provide enhanced sampling and a more representative coverage of the African continent. We studied two sub-Saharan African populations (Uganda and Angola) using the SNP forID 52-plex assay. Allele frequencies, observed heterozygosity, discrimination power and genetic distance ( F ST) between populations are reported for all markers. Comparisons revealed a low but significant genetic distance between the two populations. No significant deviations from Hardy–Weinberg equilibrium or associations between loci were detected. The forensic efficiency parameters highlight the potential of the SNP forID multiplex for identification purposes also in African populations.