Indonesia’s Marine Environment and
Region Specific Biodiversity

For convenience of both reporting and presenting recommendations, this Report will present Indonesia’s biodiversity through a composite based on the following major islands or island groups: Kalimatan (Indonesian Borneo), Sumatra, Java, Nusa Tengggara, Maluku, Sulawesi and Papua. Smaller islands and coastal marine areas for the archipelago will be associated with these above island(s). This will facilitate the selection of conservation actions that are both for the entirety of Indonesia and for specific islands or seas in the archipelago. Further, some of the above islands have similarities with those that are biogeographically closer. For this reason, Kalimantan, Sumatra and Java will be grouped under Sundaland. Kalimantan will be dealt with in slightly more detail because many of the statements on its biota will also apply to Sumatra and Java. The same will be true of the Wallacean islands, although Sulawesi will be dealt with in slightly more detail.

Indonesia’s Marine Environment

Before the descriptions of the major islands and their associated smaller islands and coastal marine communities, the broader Indonesian marine environment, coral reefs and mangrove communities will be dealt with as an opening section. This is because the extent of the Indonesian archipelago is such that a presentation focused on the major terrestrial island groupings will not capture, as a focus, the biodiversity importance of and threats to the broader expanse of oceans and reefs and mangroves in Indonesia.

Marine Environments, Coral Reefs and Mangrove Communities

Coral Reefs

Globally, coral reefs cover 12% of the ocean area, fringe one-sixth of the world’s coastlines (Birkland 1997) and contain hundreds of thousand of species of fauna and flora (Reaka-Kudla 1997). Southeast Asia is recognized as having the world’s richest marine biodiversity at the genetic, species and ecosystem level (IUNC/UNEP 1985, Kelleher et al. 1995). The “coral triangle” is an area including northern Australia, the Philippines, Indonesia and Papua New Guinea that has the highest coral diversity on Earth. The region contains more than 2000 species of near shore fishes (Briggs 1974), sea snakes, and marine mammals, and contains critical habitats and large rookeries of four species of sea turtles, all of which are on the endangered species list. For all taxa, species richness peaks in the “coral triangle” of Southeast Asia, then falls off moving east toward the Pacific (Werner, T.B. and G.R. Allen. Eds 1998).

Fifty-eight percent of the world’s reefs are reported to be threatened by human activities. Threats include terrestrial agriculture, deforestation and development that introduce large amounts of sediment, nutrients and pollution into the coastal areas (Bryant et al. 1998). These threats cause eutrification and create degraded habitats in the most productive parts of the tropical oceans that supply the majority of food biomass from the seas. Added to these threats is the overexploitation of coastal fisheries, often through unsustainable destructive fishing practices such as cyanide and blast/dynamite fishing. Further, more than 25% of the world’s coral reefs have been destroyed or seriously degraded by climate change and its related impacts, such as floods, etc.

Indonesia’s coastline, estimated to be around 81,000 km long, is ranked as the second longest in the world1. Approximately two-thirds of the Indonesian coastline is protected by coral reefs. All types of reefs are present in Indonesia, including fringing reefs, which are the most common, barrier reefs and patch reefs. These reefs also represent most of the morphological types, such as sloping reef faces, steep ‘drop offs’ and pinnacles. Although Indonesia’s population is not equally distributed, it has been estimated that between 60% to 95% of Indonesians live within 100 km of the coast (World Resources Institute, 2001). It is estimated that 80% of Indonesians living in coastal areas engage in marine resource-dependent activities, such as fishing and mariculture or related activities (WWF 1994). Fish products are an important food source and on average contribute twothirds of animal-based protein uptake in Indonesia (FAO 2000).

Indonesia has about 15% of the world’s coral reefs (Tomascik et al. 1997) and lies at the center of the world’s diversity of corals (Veron 1993), molluscs (Paulay 1997) and reef fish (Randall 1997). Indonesia has the highest number of coral species in the world, with more than 77 genera and 450 identified species of scleractinian (stony) corals (Veron 1995). Of the 25 marine sites recommended for certification as Natural World Heritage Marine sites, seven are located in Indonesia (UNESCO 2003). Indonesia has some 5.8 million km² of marine area, and its fisheries represent more than 37% of the world’s total species (NOAA 1999). The most diverse marine sites in Indonesia are those least impacted by humans. These are near Ambon and Sulawesi in eastern Indonesia, and they are about 20% more diverse than sites in the Java Sea, e.g., Pulau Kecil, G. Cemera and Karimunjawa) (Edinger et al. (1999). This is attributed to both biogeographical differences and to greater over-fishing in the Java Sea. Table 3.1 presents a recent comparison of the coral diversity for several of the most recognized areas of marine biodiversity in the world. Five of the seven regions surveyed include Indonesia, and they show the global importance of the diversity of coastal and marine regions within Indonesia to global sustainable development of marine resources.

Major causes of Indonesian coral reef degradation are bleaching events associated with elevated seawater temperatures and the El Niño Southern Oscillation (ENSO) effect (Brown and Suharsono 1990), human overexploitation, physical damage and death due to marine pollution, destructive fishing practices and proximity to major urban centers that generate pollution (Bryant et al. 1998). Of the 15 reefs studied in three regions of Indonesia (Java Sea, seven reefs; South Sulawesi, four reefs; and Ambon, four reefs) that are subject to land-based pollution, such as sewage, sediment, and/or industrial pollution, 30-50% had reduced coral diversity relative to unpolluted reference reefs in their region at a depth of 3 m, and 40-60% had reduced diversity at a depth of 10 m. Bombed or anchor-damaged reefs were similarly less diverse in shallow water at 3 m than undamaged reefs in the same areas. At 10 m depth, the relative decrease in diversity was only 10%. It is difficult to separate clearly the effects of sewage, agricultural and aquacultural runoff, sedimentation -- mainly due to erosion from logging -- and industrial effluent. In all cases, the unimpacted reference reefs in the three areas had a greater diversity than those exposed to urban and riverine pollution. At all sites, pollution had a greater negative impact on coral diversity than mechanical damage caused by, for example, anchoring on the same reefs.

Land-based pollution constitutes the greatest threat to reef coral biodiversity in Indonesia, in particular, the combination of sedimentation and nutrient loading (Edinger et al. 1999). Pollution reduces the amount of Acropora coral, one of the more important reef builders, and causes a reduction in habitat complexity. Fish diversity is directly related to habitat complexity. Therefore, the closer the survey sites are to the pollution sources, which are, primarily urban centers, the less coral cover and habitat diversity is found, with a concomitant reduction in fish diversity. Pollution effects on corals endure until the stress or source is removed. Recovery from eutrophication damage to reefs appears to require at least 10 years after restoring water quality (Maragos et al. 1985; Grigg 1995). Cesar et al. (1997) modeled the economic effects of reef degradation in Indonesia and estimated that the loss to the fishery sector alone (i.e., not including tourism) from reef degradation and over fishing to be $410,000 per km². Extrapolations from these two studies (Edinger et al. 1999 and Cesar et al. 1997), suggest that Indonesia has already lost 40% of its reef fisheries resource, yielding an estimated loss of $30 billion to the Indonesian economy over 25 years.

Biodiversity and Tropical
Forests in Indonesia
Biodiversity and Tropical Forests in Indonesia
Indonesian Biodiversity Patterns
Indonesia’s Marine Environment and
Region Specific Biodiversity
Legislative and Institutional Structure
Affecting Biological Resources
Legislative Basis for Protection and Management of Biodiversity and Forest Resources
Biodiversity Sumatra and Associated Islands
Biodiversity Kalimantan
Biodiversity Java and Associated Islands
Biodiversity Sulawesi
Biodiversity Nusa Tenggara and Maluku
Biodiversity Papua


Mangrove Forests are considered to be one of the most productive and biologically diverse wetlands on earth, providing habitats for more than 2,000 species of coastal marine flora and fauna including the endangered dugong and Indo-Pacific crocodile. Mangrove canopies also shelter hundreds of species of birds. The largest expanse of Mangrove Forests, around 20% of the world’s total, borders the Sunda Shelf, a region of Southeast Asia that includes Vietnam, Kampuchea, Thailand, Malaysia and the Indonesian islands of Sumatra, Java and Borneo. Indonesia’s Mangrove Forests remain the most extensive in the region, covering some 4.2 million hectares with about 75% of the total amount concentrated on Irian Jaya, and nearly 400,000 hectares along the south and western coasts of Kalimantan.

Source : Report on Biodiversity and Tropical Forests in Indonesia, USAID/Indonesia, 2004. Prepared by : (1) Steve Rhee, M.E.Sc. (2) Darrell Kitchener, Ph.D. (3) Tim Brown, Ph.D. (4) Reed Merrill, M.Sc. (5) Russ Dilts, Ph.D. (6) Stacey Tighe, Ph.D.

biodiversity mangrove bidiversity