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- World (World)
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- Arafura Seachannel (Seachannel)
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- Aru Sea (Sea)
- Aru Seachannel (Seachannel)
- Bali Basin (Basin)
- Bali Sea (IHO Sea Area)
- Banda Sea (IHO Sea Area)
- Berau Bay (Gulf)
- Bohol Sea (Sea)
- Bone Basin (Basin)
- Celebes Basin (Basin)
- Celebes Sea (IHO Sea Area)
- Ceram Sea (IHO Sea Area)
- Flores Basin (Basin)
- Flores Sea (IHO Sea Area)
- Gorontalo Basin (Basin)
- Gulf of Boni (IHO Sea Area)
- Gulf of Carpentaria (Gulf)
- Gulf of Thailand (IHO Sea Area)
- Gulf of Tomini (IHO Sea Area)
- Gulf of Tonkin (Gulf)
- Halmahera Basin (Basin)
- Halmahera Sea (IHO Sea Area)
- Java Sea (IHO Sea Area)
- Joseph Bonaparte Gulf (Gulf)
- Keto Knoll (Knoll(s))
- Makassar Basin (Basin)
- Makassar Strait (IHO Sea Area)
- Malacca Strait (IHO Sea Area)
- Molukka Sea (IHO Sea Area)
- Natuna Sea (Sea)
- North Banda Basin (Basin)
- Papatua Seamount (Seamount(s))
- Savu Basin (Basin)
- Savu Sea (IHO Sea Area)
- Seram Trough (Trough)
- Singapore Strait (IHO Sea Area)
- South Banda Basin (Basin)
- South China Sea (IHO Sea Area)
- South Makassar Basin (Basin)
- Stewart Bank (Bank)
- Sulawesi (Island)
- Sulawesi Sea (Sea)
- Sulu Basin (Basin)
- Sulu Sea (IHO Sea Area)
- Altnacraig Shoal (Shoal)
- Balabac Great Reefs (Reef)
- Barracuda Reef (Reef)
- Basilan Strait (Strait)
- Benrinnes Reef (Reef)
- Borneo Shoal (Reef)
- Dickins Shoal (Reef)
- Don Juan de Austria Shoals (Reef)
- Fearless Shoal (Reef)
- Gem Reef (Reef)
- Great Danger Bank (Reef)
- Hart Reef (Reef)
- Java Reef (Reef)
- Jessie Beazley Reef (Reef)
- Maeander Reef (Reef)
- Magpie Bank (Bank)
- Malaysian part of the Sulu Sea (Marine Region)
- Marabout Shoal (Shoal)
- Memnon Shoal (Reef)
- Monmouth Shoals (Reef)
- Moyune Shoal (Reef)
- Normanby Bank (Shoal)
- Northwest Danger Shoals (Reef)
- Northwest Ramos Shoal (Reef)
- Outer Shoal (Reef)
- Pasig Shoal (Reef)
- Pearl Bank (Bank)
- Pegasus Reef (Reef)
- Philippine part of the Sulu Sea (Marine Region)
- PHL-12 (HAB monitoring grid)
- Queen of the Sea Bank (Reef)
- René Shoal (Reef)
- Sentry Bank (Shoal)
- Southwest Bank (Reef)
- Southwestern Banks (Reef)
- Sultan Bank (Reef)
- Sultana Shoals (Reef)
- Sulu Trough (Trough)
- Sunday Bank (Shoal)
- Tablas Island (Island)
- Talantam Shoal (Shoal)
- Tubbataha Reefs (Reef)
- Tubbataha Reefs Natural Park (World Marine Heritage Site)
- Valparaiso Shoal (Reef)
- Wakefield Shoal (Reef)
- West Pasig Shoal (Reef)
- Willcox Bank (Bank)
- Wright Shoal (Shoal)
- Sumba Strait (Strait)
- Sunda Strait (Strait)
- Tane-Yaku Spur (Spur)
- Timorese Exclusive Economic Zone (EEZ)
- Weber Basin (Basin)
- Yaku-Shin Bank (Bank)
- Southern Ocean (IHO Sea Area)
