Marine Protected Areas
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Raja Ampat’s rich reefs and abundant seas provide a multitude of ecosystem services to local communities, along with a variety of domestic and international industries. From traditional use and food security, through to fisheries and a thriving tourism industry; a variety of stakeholders derive benefit from the regions marine resources.

In order to protect these resources from inordinate exploitation and unsustainable use, and to ensure the long-term protection of marine environments, in 2004 the first of 9 Marine Protected Areas (MPAs) was established. This network of MPAs now covers 2,000,109 hectares which together form the Raja Ampat Marine Park, under provincial and national jurisdiction.

Each Marine Protected Area contains specific zones, which help to manage and protect natural resources by applying rules that define the activities that are permitted, the activities that are prohibited, and the activities that require a permit. Zones may also place restrictions on how some activities are conducted.

Zoning is an integral component of management of Marine Protected Areas; it is a key strategy in sustaining and improving reef health and resilience, leading to healthy and productive reefs throughout the region, which in turn provides food security, regional stability, and economic and health benefits to local communities and a range of local and international stakeholders.

The Raja Ampat Marine Park Management and Zonation Plan 2019-2038 makes provision for a range of ecologically suitable commercial, recreational and research opportunities within Marine Protected Areas, along with supporting traditional usage and related practices.


The 9 Marine Protected Area & their Zones:

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Raja Ampat Marine Park Marine Protected Areas Zones Zoning

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This Zoning table outlines which activities are permitted or forbidden in each of the MPA Zones.  This zones are clearly marked on the corresponding maps for each of Raja Ampat’s Marine Protected Areas.

Arnaud Brival Yaf Keru Reef Restoration Conservation Raja Ampat

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The Dampier Strait Marine Protected Area stands as the second most expansive MPA in Raja Ampat.  Divided into three distinct regions this MPA includes the shoreline zones of Gam and Mansuar Islands, the coastal stretches of Batanta Island, and the coastal areas on the northern and northeastern parts of Salawati Island.

Where Raja Ampat is at the heart of the Coral Triangle, the Dampier Strait is at the heart of Raja Ampat.  The strait benefits from strong oceanic currents that flow from the Pacific Ocean, coupled with upwellings of deep-sea waters that carry a wealth of nutrients into the strait’s waters. This creates an ideal habitat for marine species to prosper and for coral ecosystems to thrive.

Celebrated for having the richest biodiversity across Raja Ampat, the Dampier Strait MPA is well known for its vivid coral reefs and the diverse marine life. The area serves as a magnet for large pelagic species such as sharks, tuna, snapper, grouper, barracuda, and trevally. Additionally, the Dampier Strait also provides a critical refuge and migratory pathway for various marine mammals, including whales, dolphins, and dugongs. It is notably acclaimed for it’s seasonal aggregations of both species manta ray.

Fam Islands MPA Marine Protected Area Raja Ampat | The SEA People | Conservation Raja Ampat
FAM ISLANDS MPA: 357,282ha

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Directly bordering the Halmahera Sea, the Fam Islands Marine Protected Area is distinguished by its small karst islands, and has risen in popularity and development as  tourists visiting Raja Ampat are drawn by its stunning natural landscapes both above and beneath the sea’s surface.

Among these mostly uninhabited Fami islands, three villages have been established: Fam Village on the smaller Fam island, along with Saukabu and Saupapir on the larger Fam island. In addition to these communities, there exist a few other smaller settlements functioning as business hubs or temporary housing for fisherman.

The establishment of the Fam Islands MPA was initiated by the local community, aiming to conserve the rich marine life that thrives in the waters around these islands, and this area achieved a formal declaration of the Fam Islands MPA in January 2017.

The coral reefs around the Fam Islands burst with life, hosting extensive stretches of hard coral and a variety of marine species. Predatory fish such as sharks and tuna, colorful reef fish like anthias and damsels, and ancient Tridacna Clams are found amidst the dense coral gardens. Surrounding waters serve as critical habitats for emblematic marine species, including sharks, Napoleon fish, two turtle species, both manta ray species, and marine mammals like whales and dolphins. The Fam Island MPA is also notable for housing the world’s largest land crab, the Coconut Crab (Birgus latro), a species under protection in Indonesia. Despite protective measures, there have been instances of Coconut Crabs being captured and sold, an illegal activity in Raja Ampat and across Indonesia, and punishable by law.

Asia and Ayau Islands MPA Marine Protected Area Raja Ampat | The SEA People | Conservation Raja Ampat

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Adjacent to Palau and the Philippines, the Asia Ayau Islands mark some of Indonesia’s most distant territories, with the Asia Ayau Marine Protected Area  encompassing 99,339 hectares.

This MPA features a vast coral reef bank and atoll among its island surroundings. Celebrated for hosting the most significant grouper spawning grounds in Eastern Indonesia, this sensitive ecosystem is crucial for supplying grouper fish and eggs to the Maluku and Halmahera regions, as well as extensive portions of Papua’s Bird’s Head Seascape.

The Asia Ayau Islands Archipelago serves as a critical area for economically valuable fish species including napoleon wrasse, trevally, tuna, skipjack, and other pelagic species like mackerel.  Additionally, this MPA recognized for it’s significant, highly senstive sea turtle nesting sites, accommodating both the Green Turtle (Chelonia mydas) and the Leatherback Turtle (Dermochelys coriacea).  The local waters are also home to Bottlenose dolphins (Tursiops truncatus), spinner dolphins (Stenella longirostris), and sperm whales (Khazalie et al., 2011).

Being such a remote area, communities here depend upon a continued state of reef to survive, relying heaving on fishing to survive. Given it’s location and grouper spawnings, during the 1990s, Hong Kong vessels frequented Ayau to purchase live groupers directly from the locals for export – profiting greatly from the practice whilst depleting the seas for local people.  This activity, along with destructive fishing practices like blast fishing and cyanide use, have largely ceased with the establishment of the Asia and Ayau MPA in 2007, although on occasion, illegal fishing vessels or practices occur the area.

Mayalabit Bay MPA Marine Protected Area Raja Ampat | The SEA People | Conservation Raja Ampat

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Covering an expanse of 49,451ha, the Mayalibit Bay Marine Protected Area (MPA) nearly divides the island of Waigeo in half. The bay is distinguished by its extensive mangrove forests and seagrass beds, with seagrass extending about 70 meters from the mangrove edges to the shoreline. While the presence of hard corals is limited, the bay is thought to be a crucial habitat for  economically valuable marine life such as mackerel, rabbitfish, shrimp, trevally, snapper and mud crab (Scylla), making it a critical area for marine biodiversity and conservation.

This area is markedly different from the more well known areas of Raja Ampat; a narrow mouth opens into a vast, cliff lined bay, containing large networks of mangrove and seagrass and surrounded by dense, primary rainforest. Rivers and inlets snake their way through the forest, which can occasionally be followed to their source.

Mayalibit Bay is considered the ancestral home of the Maya people, the indigenous inhabitants of Raja Ampat, residing in 11 villages and 1 hamlet within the bay.

Mayalibit Bay was officially designated as a Marine Protected Area on November 15,  2006, following a customary declaration by the Waifoi village community, and was the first MPA within Raja Ampat.

Kofiau Boo MPA Marine Protected Area Raja Ampat | The SEA People | Conservation Raja Ampat

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The Kofiau-Boo Islands Marine Protected Area (MPA), situated at Raja Ampat’s western frontier, encompasses an area of 148,979 hectares. This MPA is home to 44 islets in two clusters: the eastern Kofiau Islands and the western Boo Islands, together constituting the Kofiau District.

Renowned for its rich diversity of coral species, the area boasts an average of 292 coral species per site, showcasing an exceptional level of biodiversity for islands of its size. Coral reefs span 13,800 hectares within the MPA, while mangrove forests cover an additional 3,413 hectares.

Beyond its coral and fisheries, the Kofiau-Boo Islands MPA serves as a vital migratory passage for various cetaceans and marine mammals, including sperm whales, killer whales, bryde whales, bottlenose dolphins, Indo-Pacific bottle-nosed dolphins, and dugongs.

The indigenous population of the Kofiau-Boo Islands, descendants of the Betew Tribe, share linguistic and cultural ties with the Biak Tribe from the northern part of the Bird’s Head Seascape. The primary sources of livelihood for these communities include fishing and seasonal agricultural activities such as copra production.

In line with the broader Raja Ampat region’s practices, the local communities of the Kofiau-Boo Islands employ the traditional ‘Sasi’ resource management system. This method regulates the use of natural resources by permitting or prohibiting specific activities in designated areas to ensure sustainable management.

This approach, complemented by No Take Zones and Utilisation Zones, plays a crucial role in the enhancement and stewardship of local fisheries and marine ecosystems.

Asia and Ayau Islands MPA Marine Protected Area Raja Ampat | The SEA People | Conservation Raja Ampat

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In March 2018, the North Misool Marine Protected Area was formally acknowledged as an MPA by the local community, in partnership with Yayasan Nazareth Papua and Conservation International.  This endorsement reflected the shared vision of the Matbat and Matlou communities residing in North Misool’s nine villages, to designate 313,708 hectares of their marine territory as a conservation area.

North Misool’s marine ecosystem, though less explored compared to other regions in Raja Ampat, has been recognized for its biodiversity. The area is frequented by marine mammals such as dolphins, Bryde’s whales, orcas, and whale sharks. It’s also a critical habitat for sharks, manta rays, and notably, hosts significant populations of saltwater crocodiles in its northern rivers.

A notable conservation effort in North Misool is the dugong surveillance program initiated in 2008 by Yayasan Nazareth Papua and the community, aimed at identifying and conserving dugong feeding areas. This initiative has grown into a broader conservation project, including patrols to monitor dugong populations.

Although rich in biodiversity, North Misool faces challenges from illegal and destructive fishing practices, such as bomb and cyanide fishing, and the poaching of protected species. The area’s remoteness and limited access exacerbate governance and conservation challenges.

Mayalabit Bay MPA Marine Protected Area Raja Ampat | The SEA People | Conservation Raja Ampat

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The Misool Islands Marine Protected Area, positioned in Raja Ampat’s southernmost region, spans over 346,189 hectares. 

Renowned for its diverse marine life, the Misool Islands are especially famous for their flourishing soft coral ecosystems. The underwater landscape features rocky formations, coral pinnacles, and shelters teeming with a variety of marine life including enormous gorgonian sea fans, vibrant tunicates, swarms of jacks, barracudas, and even larger gatherings of fusiliers. Frequent sightings of groupers and reef sharks add to the area’s allure, alongside the mesmerizing presence of pygmy seahorses and diverse nudibranch species decorating the coral habitats.

The richness and diversity of the reefs are attributed to the area’s proximity to the Ceram Trough’s deep waters, which facilitate nutrient upwelling from the Indonesian Throughflow moving south towards the Banda Sea.

The MPA also features secluded beaches that are vital nesting sites for green and hawksbill turtles, regions frequented by aggregating manta rays, and river estuaries home to saltwater crocodiles.

The Misool Islands are also home to abundant mangrove forests, including rare Bluewater Mangroves, which servei as critical habitats for various fish, shrimp, and crabs, crucial for local sustenance.

In the early 2000s, the Misool Islands faced threats from destructive fishing methods. To combat this, a joint initiative in 2005 between the local community and Misool Eco Resort established the first No Take Zone. This effort has expanded into a comprehensive conservation program led by the Misool Foundation, working closely with the Raja Ampat Marine Park Authority to safeguard the area through regular patrols, radar, and drone surveillance, significantly increasing marine biomass and shark populations within the protected zones. This collaborative model, emphasizing sustainable tourism and the traditional ‘sasi’ practice, is crucial for the ongoing protection and management of the Misool Islands’ marine and terrestrial resources.

Kofiau Boo MPA Marine Protected Area Raja Ampat | The SEA People | Conservation Raja Ampat
Asia and Ayau Islands MPA Marine Protected Area Raja Ampat | The SEA People | Conservation Raja Ampat

Threats to Raja Ampat’s Reefs

With its remote location and poor accessibility, to date relative isolation and low human population (50,000 inhabitants) has been Raja Ampat’s greatest defence against overuse and exploitation.  However, rich coastal and marine resources combined with increasing accessability have made it a target for economic development activities ranging from marine tourism, through to fisheries, mining and logging.  Now, in addition to the burden of human induced climate change that is affecting reefs globally, the reefs of Raja Ampat face a series of new and emerging threats from locally developing industries.

Please visit our XXXXX page for more details regarding the threats to Raja to Raja Ampat’s Reefs. 

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