Constructing pangenome references for the improved catalogue of genomic variation is an ever-increasingly new study in human genetics to determine the true extent of human diversity and associated medical impact. Despite broad agreement that Homo sapiens originated in Africa and Khoe-San African foragers show the oldest known split date among present-day humans, they have no such study to date. Here, together with the generation of 33-55 whole-genome short-read data for 150 Khoe-San peoples, we build three reference-grade assemblies of Khoe-San individuals with a per-base accuracy of 99.999%, using integrative analysis of HiFi long-read and short-read technologies. While short-read data reveal ~30 million small-to-large variants with >1.3 million single nucleotide variants being novel, pangenome inference of three Khoe-San and 44 public pangenome drafts identifies ~900 thousand additional novel variants in the foragers. Khoe-San genomic variants identify ‘San’ and ‘Damara’ as separate phylogenetic lineages, representing shared traditionally forager lifestyles and click-speaking languages. While San represents modern humans’ deep divergence (~115 thousand years ago), Damara divergence is recent; both show high effective population size estimates suggesting global dominance between 45-150 thousand years ago. Developing assembly-based selection tests, we extensively report 1,376 genes under positive selection (dN/dS = 19.46), of which 479 are significantly associated with forager peoples and, therefore, maintained ancestral alleles that differ from derived genetic variation observed in non-Africans. Using our pangenome drafts, the pathway analysis of 2,276 new truncated variants shows three significant pathways (FDR <0.04998) involved in megabase regions of HLA, OR and KRT/KRTAP forager-associated multigene families, with their phylogenies and relevant long-read methylation suggesting the evolutionary mode of gene copy gain or loss. This work provides a first draft of African forager pangenomes and confirms its accurate detection of early diverged genetic variation and relevant epigenetic discovery to establish the full extent of global reference resources.