Fishes:
- Amur sturgeon (Acipenser schrenckii, formerly in Dunia Air Tawar)
- Common carp (Cyprinus carpio, almost all Indonesian zoos and aquaria)
- Grass carp (Ctenopharyngodon idella, Dunia Air Tawar)
- Silver carp (Hypophthalmichthys molitrix, formerly in Dunia Air Tawar)
- Largemouth bronze gudgeon (Coreius guichenoti, privately owned)
- Chinese phoenix barb (Spinibarbus denticulatus, privately owned)
- Yellowcheek (Elopichthys bambusa, privately owned)
- Chinese high-fin banded shark (Myxocyprinus asiaticus, Dunia Air Tawar and formerly in SeaWorld Ancol)
- Goldfish (Carassius auratus, almost all Indonesian zoos and aquaria)
- Weather loach (Misgurnus anguillicaudatus, privately owned)
- Imperial flower loach (Leptobotia elongata, privately owned)
- Golden barb (Barbodes semifasciolatus, Dunia Air Tawar)
- White Cloud Mountain minnow (Tanichthys albonubes, privately owned)
- Mandarin perch (Siniperca scherzeri, privately owned)
- Paradisefish (Macropodus opercularis, formerly in Dunia Air Tawar)
- Taiwanese snakehead (Channa asiatica, privately owned)
- Blotched snakehead (Channa maculata, privately owned)
- Northern snakehead (Channa argus, privately owned)
- Giant mottled eel (Anguilla marmorata, Jakarta Aquarium and formerly in Dunia Air Tawar and SeaWorld Ancol)
- Chinese largemouth catfish (Silurus meridionalis, privately owned)
- Chinese longsnout catfish (Tachysurus longirostris, privately owned)
- Shuttles mudskipper (Periophthalmus modestus, Jakarta Aquarium)
- Cherry anthias (Sacura margaritacea, Jakarta Aquarium)
- Spangled emperor (Lethrinus nebulosus, Jakarta Aquarium)
- Waigieu seaperch (Psammoperca waigiensis, formerly in SeaWorld Ancol)
- Azurio tuskfish (Choerodon azurio, formerly in SeaWorld Ancol)
- Snubnose dart (Trachinotus blochii, almost in all Indonesian aquaria)
- Bigeye trevally (Caranx sexfasciatus, almost in all Indonesian aquaria)
- Bluefin trevally (Caranx melampygus, SeaWorld Ancol)
- Manybar goatfish (Parupeneus multifasciatus, formerly in Jakarta Aquarium)
- Pineconefish (Monocentris japonica, SeaWorld Ancol and formerly in Jakarta Aquarium)
- False kelpfish (Sebastiscus marmoratus, formerly in Jakarta Aquarium)
- Longspine snipefish (Macroramphosus scolopax, Jakarta Aquarium)
- Eyelightfish (Photoblepharon palpebratum, formerly in Jakarta Aquarium)
- Giant moray (Gymnothorax javanicus, almost all Indonesian aquaria)
- Slender giant moray (Strophidon sathete, formerly in SeaWorld Ancol)
- Dagger-tooth pike conger (Muraenesox cinereus, privately owned)
- Bastard halibut (Paralichthys olivaceus, formerly in SeaWorld Ancol)
- Sand tiger shark (Carcharias taurus, formerly in SeaWorld Ancol and soon in PIAMARI)
- Scalloped hammerhead shark (Sphyrna lewini, SeaWorld Ancol)
- Sandbar shark (Carcharhinus plumbeus, soon in PIAMARI)
- Common shovelnose ray (Glaucostegus typus, Jakarta Aquarium and formerly in SeaWorld Ancol)
- Red stingray (Hemitrygon akajei, Jakarta Aquarium)
- Chinese giant salamander (Andrias davidianus, privately owned)
- Oriental fire-bellied newt (Cynops orientalis, formerly in Dunia Air Tawar)
- Oriental fire-bellied toad (Bombina orientalis, privately owned)
- Chinese pond turtle (Mauremys reevesii, privately owned)
- Chinese stripe-necked turtle (Mauremys sinensis, formerly in Museum Komodo)
- Chinese three-striped box turtle (Cuora trifasciata, privately owned)
- Indochinese box turtle (Cuora galbinifrons, privately owned)
- Chinese softshell turtle (Pelodiscus sinensis, Bandung Zoo and formerly in Museum Komodo and Dunia Air Tawar)
- Elongated tortoise (Indotestudo elongata, privately owned)
- Chinese crocodile lizard (Shinisaurus crocodilurus, privately owned)
- Chinese water dragon (Physignathus cocincinus, Batu Secret Zoo)
- Hainanese bird spider (Cyriopagopus hainanus, privately owned)
- Chinese red-headed centipede (Scolopendra subspinipes mutilans, Jakarta Aquarium and Dunia Serangga)
- Giant water bug (Lethocerus deyrollei, Dunia Serangga)
- Japanese rhinoceros beetle (Trypoxylus dichotomus, privately owned)
- Tri-spine horseshoe crab (Tachypleus tridentatus, formerly in SeaWorld Ancol)
- Giant isopod (Bathynomus giganteus, Jakarta Aquarium)
- Japanese spider crab (Macrocheira kaempferi, formerly in SeaWorld Ancol)
- Gazami crab (Portunus trituberculatus, formerly in SeaWorld Ancol)
- Crucifix crab (Charybdis feriata, formerly in SeaWorld Ancol)
- Japanese mitten crab (Eriocheir japonica, formerly in Jakarta Aquarium)
- Japanese slipper lobster (Parribacus japonicus, formerly in SeaWorld Ancol)
- Amano shrimp (Caridina multidentata, privately owned)
- Cherry shrimp (Neocaridina davidi, formerly in Dunia Air Tawar)
- Giant Pacific octopus (Enteroctopus dofleini, formerly in Jakarta Aquarium and SeaWorld Ancol)
- Common octopus (Octopus vulgaris, formerly in Jakarta Aquarium)
- Bigfin reef squid (Sepioteuthis lessoniana, formerly in Jakarta Aquarium)
- Broadclub Cuttlefish (Sepia latimanus, formerly in Jakarta Aquarium)
- Chambered nautilus (Nautilus pompilius, Jakarta Aquarium and formerly in SeaWorld Ancol)
- Chinese pond mussel (Sinanodonta woodiana, formerly in Dunia Air Tawar)
- Blue bat star (Patiria pectinifera, Jakarta Aquarium)
- Sea apple (Pseudocolochirus violaceus, formerly in SeaWorld Ancol)
- Flower hat jelly (Olindias formosus, Jakarta Aquarium)
- Moon jelly (Aurelia aurita, Jakarta Aquarium and SeaWorld Ancol)
- Peregrine falcon (Falco peregrinus, Faunaland Ancol)
- Barn owl (Tyto alba, almost all Indonesian zoos and aquaria)
- Eurasian eagle-owl (Bubo bubo, Lembang Zoo & Park and formerly in Taman Safari Cisarua)
- Chinese goose (Anser cygnoides, almost all Indonesian zoos)
- Pekin duck (Anas platyrhynchos domesticus, Taman Safari Cisarua and Farmhouse Lembang)
- Mandarin duck (Aix galericulata, almost all Indonesian bird parks)
- Demoiselle crane (Grus virgo, Taman Safari Cisarua)
- Purple heron (Ardea purpurea, Taman Safari Cisarua and Eco Green Park)
- Black-crowned night heron (Nycticorax nycticorax, Bandung Zoo, Taman Safari Cisarua and Taman Burung TMII)
- Green peafowl (Pavo muticus, almost all Indonesian zoos)
- Ring-necked pheasant (Phasianus colchicus, Siantar Zoo)
- Golden pheasant (Chrysolophus pictus, Taman Safari Cisarua)
- Lady Amherst's Pheasant (Chrysolophus amherstiae, privately owned)
- Silver pheasant (Lophura nycthemera, Taman Safari Cisarua)
- Japanese quail (Coturnix japonica, Farmhouse Lembang)
- Giant panda (Ailuropoda melanoleuca, Taman Safari Cisarua)
- Asian black bear (Ursus thibetanus, Taman Safari Prigen)
- Eurasian brown bear (Ursus arctos arctos, Taman Safari Cisarua)
- Snow leopard (Panthera uncia, Batu Secret Zoo and formerly in Taman Safari Cisarua)
- Siberian tiger (Panthera tigris altaica, Batu Secret Zoo)
- Mainland clouded leopard (Neofelis nebulosa, Batu Secret Zoo)
- Tsushima leopard cat (Prionailurus bengalensis euptilurus, privately owned)
- Chinese red panda (Ailurus fulgens styani, Taman Safari Cisarua)
- Masked palm civet (Paguma larvata, Farmhouse Lembang)
- Large bamboo rat (Rhizomys sumatrensis, Taman Safari Cisarua)
- Chinese bamboo rat (Rhizomys sinensis, privately owned)
- Chinese hamster (Cricetulus griseus, Taman Safari Cisarua)
- Dzungarian hamster (Phodopus sungorus, privately owned)
- Bactrian camel (Camelus bactrianus, Taman Safari Cisarua and Prigen)
- Mishmi takin (Budorcas taxicolor taxicolor, Taman Safari Cisarua)
- Wild boar (Sus scrofa, formerly in Bali Zoo)
- Japanese macaque (Macaca fuscata, Taman Safari Cisarua)
- Steller sea lion (Eumetopias jubatus, formerly in Ocean Dream Samudra and Taman Safari Cisarua)
- Indo-Pacific bottlenose dolphin (Tursiops aduncus, Ocean Dream Samudra, Taman Safari Cisarua, Batang Dolphin Center, and Taman Safari Prigen)
- False killer whale (Pseudorca crassidens, formerly in Ocean Dream Samudera)
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