| Cape PorcupineHystrix africaeaustralis | Hystricidae | 149 | 1 933 | LC | Hottentots-Holland |
| Xeric Four-striped Grass RatRhabdomys pumilio | Muridae | 90 | 951 | LC | Sam Knott Nature Reserve |
| Cape Dune Mole-ratBathyergus suillus | Bathyergidae | 40 | 507 | LC | False Bay Nature Reserve |
| Smith's Bush SquirrelParaxerus cepapi | Sciuridae | 37 | 734 | LC | Kruger National Park |
| Southern African Vlei RatOtomys irroratus | Muridae | 33 | 191 | LC | Lower Guinea-Fowl Trail |
| Southern African Mole-ratCryptomys hottentotus | Bathyergidae | 24 | 139 | LC | Lower Guinea-Fowl Trail |
| Eastern Gray SquirrelSciurus carolinensis | Sciuridae | 22 | 1 185 | LC | Lion's Head Hiking Trail |
| South African Ground SquirrelXerus inauris | Sciuridae | 21 | 302 | LC | Mountain Zebra National Park |
| Cape Mole-ratGeorychus capensis | Bathyergidae | 20 | 92 | LC | Tokai Park |
| Greater Cane RatThryonomys swinderianus | Thryonomyidae | 18 | 61 | LC | iSimangaliso Wetland Park |
| Namaqua MicaelamysMicaelamys namaquensis | Muridae | 16 | 237 | LC | Augrabies Falls National Park |
| Red Bush SquirrelParaxerus palliatus | Sciuridae | 16 | 170 | LC | iSimangaliso Wetland Park |
| Bush Karroo RatMyotomys unisulcatus | Muridae | 14 | 79 | LC | Addo Elephant National Park |
| Southern African Pygmy MouseMus minutoides | Muridae | 12 | 31 | LC | uMkhuze Game Reserve |
| South African Spring HarePedetes capensis | Pedetidae | 12 | 98 | LC | Kruger National Park |
| Southern African Pouched MouseSaccostomus campestris | Nesomyidae | 12 | 58 | LC | Augrabies Falls National Park |
| Forest African DormouseGraphiurus murinus | Gliridae | 9 | 34 | LC | Lower Guinea-Fowl Trail |
| Cape Short-tailed GerbilDesmodillus auricularis | Muridae | 7 | 34 | LC | The Koppie Nature Reserve |
| Single-Striped LemniscomysLemniscomys rosalia | Muridae | 6 | 27 | LC | T.C. Robertson Nature Reserve |
| Common GrammomysGrammomys dolichurus | Muridae | 6 | 18 | LC | Lower Guinea-Fowl Trail |
| Paeba Hairy-footed GerbilGerbillurus paeba | Muridae | 6 | 156 | LC | The Koppie Nature Reserve |
| Red Veld AethomysAethomys chrysophilus | Muridae | 5 | 49 | LC | uMkhuze Game Reserve |
| Natal MastomysMastomys natalensis | Muridae | 5 | 123 | LC | Lydenburg Natuurreservaat |
| Mesic Four-striped Grass RatRhabdomys dilectus | Muridae | 4 | 8 | LC | Pledge Nature Reserve |
| Southern African MastomysMastomys coucha | Muridae | 3 | 90 | LC | Sam Knott Nature Reserve |
| Angoni Vlei RatOtomys angoniensis | Muridae | 3 | 8 | LC | Lydenburg Natuurreservaat |
| Southern African Spiny MouseAcomys spinosissimus | Muridae | 3 | 14 | LC | Lydenburg Natuurreservaat |
| Southern Giant Pouched RatCricetomys ansorgei | Nesomyidae | 3 | 6 | LC | Medike Mountain Sanctuary |
| Black-tailed ThallomysThallomys nigricauda | Muridae | 3 | 9 | LC | Kgalagadi Transfrontier Park |
| Brants's African Climbing MouseDendromus mesomelas | Nesomyidae | 3 | 14 | LC | Muizenberg Cave |
| South East African Vlei RatOtomys auratus | Muridae | 3 | 7 | NT | Korsman Conservancy |