The Onganja copper deposit is hosted by quartz-biotite-plagioclase schists of the Kuiseb Formation in the Southern Zone or Khomas trough of the Damara Orogen in Namibia. It comprises a sheeted-vein complex (3500 x 1800m) situated orthogonally in the core of a shallow-plunging D3 antiform. The vein complex consists of central calcite-dominant and peripheral quartz-dominant veins with pyrite-magnetite-chalcopyrite-apatite-molybdenite-native gold ore mineralogy. Adjacent alteration comprises proximal albite (Ab >97) and early/distal scapolite (Me 41 to 51) − biotite zones. Chlorite geothermometry indicates temperatures in the range 252 to 364 oC for the albite alteration whereas temperatures >400 oC are estimated for the scapolite-biotite zone. Stable isotope values from calcite, pyrite and chalcopyrite in the veins are: δ13C −7.9 to −6.4‰ (V-PDB), δ18O +11.6 to +12.1‰ (V-SMOW), δ34S +3.6 to +8.9‰ (V-CDT). Re-Os dating of molybdenite from two veins gave ages of 517 ± 3 and 518 ± 3 Ma. Late-stage supergene chalcocite-brochantite enrichment is related to the African erosion cycle. The Onganja copper deposits formed from NaCl-CO2-rich metamorphogenic hydrothermal fluids at a late stage (late to post-D3) in the Damara orogenic cycle, subsequent to the intrusion of the Donkerhuk Granite pluton in the northern Southern Zone. Comparison is made to other Pan-African deposits in the Southern and southern Central Zones of the Damara Orogen and the Lufilian Orogen in Zambia, specifically with the Navachab Au and Kansanshi Cu deposits. The Onganja deposit is shown to be the final phase of a protracted history of copper mineralization across the entire development and deformation of the Southern Zone.