From WWF - MPA Forum - South Africa website:

In South Africa all MPA’s are ultimately managed by the South African Government who have agreements with various MPA Management Authorities like South African National Parks (SANParks), CapeNature, Eastern Cape Parks and Tourism Agency (ECPTA), KZN Wildlife, Nelson Mandela Bay Metro (NMBM) and the City of Cape Town (CoCT).

Most South African MPA’s are attached to a National Park or Nature Reserve and that Management Authority then also manages the attached MPA with funding from the SA Government channelled through its Department of Environmental Affairs (DEA) giving the Management Authorities the mandate to manage the day to day running of the MPA and its staff.

South African MPA Zonation’s

In SA the MPA’s can be categorised into three classifications as per the MLRA (Marine Living Resources Act);

1. Restricted Area 
These are complete or specific section/s within a marine protected area also commonly known as ‘No-Take’ areas, which is where the extraction and harvesting of all marine and plant life is prohibited.
De Hoop and Tsitsikama MPAs, for example, are zoned as a Restricted Areas, making them complete No-Take zones.

2. Controlled Area
These are specific sections within a marine protected areas also known as ‘Open’ areas where you are allowed to extract and harvest marine life, on condition that you have a valid permit allowing you to practice one of the following specific activities: spear fishing, angling, scuba diving, snorkelling for mollusc extraction, boating, commercial diving, salvage operations, commercial fishing, whale watching, shark cage diving or filming.

3. Restricted and Controlled Areas
Some MPAs have specifically demarcated areas that are zoned as both Restricted and Controlled areas. These allow management control on the restriction of marine extraction from the Restricted Areas and the extraction of marine resources under a permit from the Controlled Areas. An example of this is the Table Mountain National Park MPA which has 6 Restricted Areas within the MPA area of approx. 1000Km2 with the remainder of the MPA zoned as a Controlled Area.

More about the MPA's here

More Information:

The danger of SA's watered-down marine protections (9 Sept 2018) Business Day

334 MPAs:

Abjoel Inshore Controlled Zone
Abyss Restricted Zone
Addo Elephant Marine Protected Area Marine Protected Area
Adlams Controlled Catch and Release Zone
Africana II Rise Restricted Zone
Agulhas Bank Restricted Zone
Agulhas Bank Complex Controlled Zone
Agulhas Bank Complex Marine Protected Area Marine Protected Area
Agulhas Bank Deep Reefs
Agulhas Front Restricted Zone
Agulhas Front Marine Protected Area
Agulhas Front Marine Protected Area Marine Protected Area
Agulhas Mud Sanctuary Zone
Agulhas Muds Marine Protected Area Marine Protected Area
Algoa Bay Black Rocks Provincial Nature Reserve Nature Reserve
Algoa Bay Seal Island Provincial Nature Reserve Nature Reserve
Aliwal Shoal Marine Protected Area [OLD] Marine Protected Area
Aliwal Shoal Offshore Restricted Zone
Aliwal Shoal Offshore Controlled-Pelagic Linefish Zone
Aliwal Shoal - Offshore Controlled Pelagic Linefish Zone [OLD] Marine Protected Area
Aliwal Shoal - Offshore Restricted Zone [OLD] Marine Protected Area
Aliwal Shoal [OLD] Marine Protected Area
Alphard Banks Controlled Pelagic Linefish Zone
Amathole Marine Protected Area [OLD] Marine Protected Area
Amathole Offshore Marine Protected Area - Controlled Pelagic Linefish Zone [OLD] Marine Protected Area
Amathole Offshore Marine Protected Area - Controlled Zone [OLD] Marine Protected Area
Amathole Offshore Marine Protected Area [OLD] Marine Protected Area
Amathole Offshore Marine Protected Area - Restricted Zone [OLD] Marine Protected Area
Amatikulu Inshore Restricted Zone
Annet Private Nature Reserve Nature Reserve
Annex Arch Rock Private Nature Reserve Nature Reserve
Argentina Seamount Restricted Zone
Bamboeskamp Inshore Controlled Zone
Beachwood Mangroves Provincial Nature Reserve
Benguela Bank Marine Protected Area
Benguela Muds Controlled Large Pelagic Zone
Benguela Muds Marine Protected Area Marine Protected Area
Betty's Bay Controlled Zone
Betty's Bay Marine Protected Area Marine Protected Area
Bhanga Nek Controlled Zone
Bird Island Offshore Restricted Zone
Bitterrivier Inshore Restricted Zone
Black Rock Controlled Zone
Blombos Private Nature Reserve Nature Reserve
Bojaansklip Private Nature Reserve Nature Reserve
Bot - Kleinmond Estuarine System Ramsar Site, Wetland of International Importance
Boulderbaai Inshore Restricted Zone
Boulderbaai Inshore Controlled Zone
Boulders Restricted Zone
Brenton Blue Butterfly Nature Reserve Special Nature Reserve
Brian Mansergh Private Nature Reserve Nature Reserve
Browns Bank Central Zone
Browns Bank Complex Marine Protected Area
Browns Bank Corals Marine Protected Area Marine Protected Area
Browns Bank North Zone
Browns Bank South Zone
Cannon Rocks inshore Controlled Zone
Cannon Rocks Offshore Controlled Zone
Cape Canyon Restricted Zone
Cape Canyon Marine Protected Area Marine Protected Area
Cape Henderson Nature Reserve Forest Nature Reserve
Cape of Good Hope Restricted Zone
Cape of Good Hope Nature Reserve Nature Reserve
Cape Padrone inshore Controlled Zone
Cape Recife Nature Reserve Nature Reserve
Cape St. Francis Provincial Nature Reserve Nature Reserve
Cape Vidal Controlled Zone
Cape Vidal Controlled Catch and Release Zone
Castle Rock Restricted Zone
Castle Rock Restricted Zone Marine Protected Area
Central Controlled Zone
Childs Bank Controlled Large Pelagic Zone
Childs Bank Marine Protected Area Marine Protected Area
Columbine Nature Reserve Nature Reserve
Crown Offshore Restricted Zone
Dassen Island Nature Reserve Ramsar Site, Wetland of International Importance
Dassen Island Provincial Nature Reserve Nature Reserve
De Hoop Restricted Zone
De Hoop Marine Protected Area Marine Protected Area
Delagoa Offshore - St Lucia and Mapualand (Offshore and southern extension)
Delwerskamp Inshore Controlled Zone
Die Duine Private Nature Reserve Nature Reserve
Dog Point Restricted Zone
Duikerklip Provincial Nature Reserve Nature Reserve
Duin-'n-See Private Nature Reserve Nature Reserve
Duivenhoksriviermond Private Nature Reserve Nature Reserve
Dwesa-cwebe Provincial Nature Reserve
Dwesa-Cwebe Marine Protected Area Marine Protected Area
Dyer Island Provincial Nature Reserve Nature Reserve
Dyer Island Provincial Nature Reserve and Geyser Island Provincial Nature Reserv Ramsar Site, Wetland of International Importance
Eastford Private Nature Reserve Nature Reserve
Eiland Punt Inshore Controlled Zone
Elephant Rock Provincial Nature Reserve Nature Reserve
False Bay Nature Reserve Nature Reserve
False Bay Nature Reserve Ramsar Site, Wetland of International Importance
False Bay Seal Island Provincial Nature Reserve Nature Reserve
Featherbed Private Nature Reserve Nature Reserve
First Rocks Controlled Catch and Release Zone
Franscois and Annelle Marits Private Nature Reserve Nature Reserve
Freshwater Sands Private Nature Reserve Nature Reserve
Geelkrans Restricted Zone
Geelkrans Nature Reserve Forest Nature Reserve
Geelkrans Provincial Nature Reserve Nature Reserve
Geyser Island Provincial Nature Reserve Nature Reserve
Gonubie Inshore Controlled Zone
Goukamma Controlled Zone
Goukamma Estuary Controlled Zone
Goukamma Estuary Restricted Zone
Goukamma Marine Protected Area Marine Protected Area
Goukamma Offshore Restricted Zone
Goukamma Provincial Nature Reserve Nature Reserve
Goukou Estuarine Controlled Zone
Goukou Estuarine Restricted Zone
Greater St Lucia Wetland Nature Reserve Provincial Nature Reserve
Green Point Inshore Restricted Zone
Groenkant Private Nature Reserve Nature Reserve
Groenrivier Inshore Restricted Zone
Groot Dam Private Nature Reserve Nature Reserve
Groot Paternoster Private Nature Reserve Nature Reserve
Gulu Nature Reserve Forest Nature Reserve
Gxulu Inshore Controlled Zone
Gxulu Offshore Restricted Zone
Gxulu Offshore Controlled Pelagic Linefish Zone
Gxulu Offshore Controlled Zone
Helderberg Restricted Zone
Helderberg Marine Protected Area Marine Protected Area
Hluleka Restricted Zone
Hluleka Marine Protected Area Marine Protected Area
Hoek van de Berg Private Nature Reserve Nature Reserve
Huisklip Nature Reserve Nature Reserve
Illovo Offshore Controlled Zone
Inshore Controlled Zone C
Inshore Controlled Zone B
Inshore Controlled Zone A
Inshore Controlled Zone D
Inshore Controlled Zone E
Inshore Restricted Zone B
Inshore Restricted Zone C
Inshore Restricted Zone A
Inshore Restricted Zone D
Irma Booysen Flora Reserve Nature Reserve
iSimangaliso Inshore Wilderness Zone
iSimangaliso Marine Protected Area Marine Protected Area
iSimangaliso Offshore Controlled Pelagic Linefish Zone North
iSimangaliso Offshore Restricted Zone North
iSimangaliso Offshore Wilderness Zone
iSimangaliso Offshore Restricted Zone South
iSimangaliso Offshore Controlled Pelagic Linefish Zone South
Jaar se Baai Inshore Restricted Zone
Jacob's Rock Provincial Nature Reserve Nature Reserve
Jakkalsfontein Private Nature Reserve Nature Reserve
Joan Muirhead Nature Reserve Nature Reserve
Jongensgat Private Nature Reserve Nature Reserve
Jutten Island Controlled Zone
Jutten Island Marine Protected Area Marine Protected Area
Kanon Private Nature Reserve Nature Reserve
Karbonkelberg Restricted Zone
Kei Inshore Controlled Zone
Kei Offshore Restricted Zone
Kei Offshore Controlled Zone
Kleinbaai Private Nature Reserve Nature Reserve
Kleinmond Coastal Nature Reserve Nature Reserve
Knysna National Lake Area Protected Environment
Kosi Controlled Zone
Kosi Restricted Zone
Kromensee Nature Reserve Nature Reserve
Kwas se Baai Inshore Restricted Zone
Kwelanga Private Nature Reserve Nature Reserve
Lake Pleasant Private Nature Reserve Section No.2 Nature Reserve
Lake Pleasant Private Nature Reserve Section No.4 Nature Reserve
Lake Pleasant Private Nature Reserve Section No.5 Nature Reserve
Lala Nek Restricted Zone
Lambert's Bay Penguin Island Provincial Nature Reserve Nature Reserve
Langebaan Lagoon Controlled Zone
Langebaan Lagoon Sanctuary Zone
Langebaan Lagoon Restricted Zone
Langebaan Lagoon Marine Protected Area Marine Protected Area
Langebaan Nature Area Nature Reserve
Langverwacht Private Nature Reserve Nature Reserve
Leven Controlled Catch and Release Zone
Lighthouse Controlled Zone
Mabibi Controlled Zone
Malgas Island Controlled Zone
Malgas Island Marine Protected Area Marine Protected Area
Maputaland Marine Reserve Nature Reserve
Marcus Island Controlled Zone
Marcus Island Marine Protected Area Marine Protected Area
Mission Rocks Controlled Catch and Release Zone
Mosselbankfontein Private Nature Reserve Nature Reserve
Mossel Bay Seal Island Provincial Nature Reserve Nature Reserve
Msiki Restricted Zone
Mtunzini Inshore Controlled Zone
Nahoon Local Authority Nature Reserve Nature Reserve
Namaqua Fossil Forest Controlled Zone
Namaqua Fossil Forest Marine Protected Area Marine Protected Area
Namaqua National Park Marine Protected Area Marine Protected Area
Namaqua National Park Offshore Restricted Zone
Natal Seamount Restricted Zone
Ngane Offshore Restricted Zone
Nine Mile Restricted Zone
North Restricted Zone
Northern Restricted Zone
Northern Controlled Zone
Offshore Restricted Zone
Offshore Controlled Zone A
Offshore Controlled Zone B
Offshore Restricted Zone
Orange River Mouth Nature Reserve Nature Reserve
Orange Shelf Edge East Sanctuary Zone
Orange Shelf Edge Marine Protected Area Marine Protected Area
Orange Shelf Edge West Sanctuary Zone
Orca Private Nature Reserve Nature Reserve
Oubos-Grootrivier Nature Reserve Nature Reserve
Oyster Bay Private Nature Reserve Nature Reserve
Park Rynie Offshore Controlled Zone
Paternoster Rocks Provincial Nature Reserve Nature Reserve
Pauline Bohnen Nature Reserve Nature Reserve
Paulsberg Restricted Zone
Perriers Restricted Zone
Policeman’s helmet Inshore Controlled Zone
Pondoland Marine Protected Area Marine Protected Area
Port Elizabeth Corals Controlled Large Pelagic Zone
Port Elizabeth Corals Marine Protected Area Marine Protected Area
Port Elizabeth Shelf and Shelf Edge Marine Protected Area
Postberg Nature Reserve Nature Reserve
Potters Pass Nature Reserve Nature Reserve
Prince Edward Island Restricted Zone
Prince Edward Island Controlled Zone
Prince Edward Island Sanctuary Zone
Prince Edward Island Marine Protected Area [OLD] Marine Protected Area
Prince Edward Islands - Control Zones [OLD] Marine Protected Area
Prince Edward Islands - Restricted Zones (AB) [OLD] Marine Protected Area
Prince Edward Islands - Restricted Zones (AR, PEI, SIR) [OLD] Marine Protected Area
Prince Edward Islands - Sanctuary Zone [OLD] Marine Protected Area
Produce Restricted Zone
Protea Banks Controlled Zone
Protea Banks Controlled-Pelagic Linefish Zone
Protea Banks Restricted Zone
Protea Banks Marine Protected Area - Controlled Pelagic Linefish Zone [OLD] Marine Protected Area
Protea Banks Marine Protected Area - Controlled Zone [OLD] Marine Protected Area
Protea Banks Marine Protected Area [OLD] Marine Protected Area
Protea Banks Marine Protected Area - Restricted Zone [OLD] Marine Protected Area
Protea Seamount (West) Controlled Zone
Quoin Rock Provincial Nature Reserve Nature Reserve
Railway Ledges Restricted Zone
Rebelsrus Private Nature Reserve Nature Reserve
Richards Bay Provincial Nature Reserve
Robben Island Restricted Zone
Robben Island Inner Controlled Zone
Robben island Marine Protected Area Marine Protected Area
Robben Island Middle Controlled Zone
Robben Island Offshore Controlled Zone
Robberg Controlled Zone
Robberg Coastal Corridor Protected Environment Protected Environment
Robberg Marine Protected Area Marine Protected Area
Robberg Nature Reserve Nature Reserve
Rocherpan Controlled Zone
Rocher Pan Marine Protected Area Marine Protected Area
Rocky Bay Inshore Restricted Zone
Rooi Els Nature Reserve Nature Reserve
Rooisand Provincial Nature Reserve Nature Reserve
Sardinia Bay Restricted Zone
Sardinia Bay Marine Protected Area Marine Protected Area
Sardinia Bay Nature Reserve Nature Reserve
SAS Saldanha Provincial Nature Reserve Nature Reserve
Saxon Restricted Zone
Scottburgh Inshore Controlled zone
Seal Ledges Provincial Nature Reserve Nature Reserve
Sinclair Nature Reserve Forest Nature Reserve
Sixteen Mile Beach Controlled Zone
Sixteen Mile Beach Marine Protected Area Marine Protected Area
Skulpiesbaai Restricted Zone
Skulpiesbaai Local Nature Reserve Nature Reserve
Slope Seamount (East) Controlled Zone
Sodwana Controlled Zone
Sodwana Diving Restricted Zone
Southeast Atlantic Seamount Marine Protected Area Marine Protected Area
Southern Controlled Zone
Southern Restricted Zone
Southwest Indian Ridge Restricted Zone
Southwest Indian Seamount Marine Protected Area
St Croix Island Offshore Restricted Zone
Steenboksfontein Private Nature Reserve Nature Reserve
Stilbaai Marine Protected Area Marine Protected Area
Stillbaai Controlled Zone
St James Restricted Zone
St Lucia Controlled Zone
St. Lucia Marine Reserve Nature Reserve
Sundays Inshore Restricted Zone
Sundays Inshore Controlled Zone
Sundays Offshore Controlled Zone
Sundays River Estuary Restricted Zone
Sundays River Estuary Controlled Zone
Sylvic Nature Reserve Nature Reserve
Table Mountain National Park Controlled Zone
Table Mountain National Park Marine Protected Area Marine Protected Area
The Lagoon 2 Private Nature Reserve Nature Reserve
Trafalgar Marine Protected Area Marine Protected Area
Trafalgar Marine Reserve Nature Reserve
Trafalgar Offshore Controlled Zone
Tsitsikamma Restricted Zone
Tsitsikamma National Park
Tsitsikamma Coastal Control Zone 1
Tsitsikamma Coastal Control Zone 2
Tsitsikamma Coastal Control Zone 3
Tsitsikamma Marine Protected Area Marine Protected Area
Tugela Bank off KZN
Umkomaas Inshore Controlled Zone
Umlalazi Provincial Nature Reserve
Umtamvuna Provincial Nature Reserve
uSetheni Inshore Restricted Zone
uThukela Inshore Controlled Zone
uThukela Marine Protected Area [OLD] Marine Protected Area
uThukela Offshore Controlled Commercial Zone
uThukela Offshore Controlled Zone North
uThukela Offshore Controlled-Pelagic Linefish Zone
uThukela Offshore Restricted Zone
uThukela Offshore Controlled Zone South
uThukela - Offshore Controlled Commercial Zone [OLD] Marine Protected Area
uThukela - Offshore Controlled Pelagic Linefish Zone [OLD] Marine Protected Area
uThukela - Offshore Controlled Zone North [OLD] Marine Protected Area
uThukela - Offshore Controlled Zone South [OLD] Marine Protected Area
uThukela - Offshore Restricted Zone [OLD] Marine Protected Area
Vergaderingskop Private Nature Reserve Nature Reserve
Vondeling Island Provincial Nature Reserve Nature Reserve
Walker Bay Whale Restricted Zone
Walker Bay Whale Sanctuary Zone
Walker Bay Whale Sanctuary Marine Protected Area Marine Protected Area
West Coast National Park National Park
Wilderness National Lake Area Protected Environment
Witsand Local Nature Reserve Nature Reserve
Wolfgat Nature Reserve Nature Reserve
Woody Cape Nature Reserve Forest Nature Reserve
Yzerfontein Local Nature Reserve Nature Reserve

13 Marine Managed Areas:

Between Prince Edward Islands and Crozet Islands
De Hoop Vlei Wetlands of International Importance (Ramsar)
De Mond (Heuningnes Estuary) Wetlands of International Importance (Ramsar)
iSimangaliso Wetland Park World Heritage Site (natural or mixed)
Kosi Bay Wetlands of International Importance (Ramsar)
Lake Sibaya Wetlands of International Importance (Ramsar)
Langebaan Wetlands of International Importance (Ramsar)
Orange River Mouth Wetlands of International Importance (Ramsar)
Plett Hope Spot
St. Lucia System Wetlands of International Importance (Ramsar)
Turtle Beaches/Coral Reefs of Tongaland Wetlands of International Importance (Ramsar)
Verlorenvlei Wetlands of International Importance (Ramsar)
Wilderness Lakes Wetlands of International Importance (Ramsar)