Mammal
* Black-striped squirrel (Callosciurus nigrovittatus) at Taman Mini Indonesia Indah, no longer on display
* Javan mongoose (Herpestes javanicus) at Taman Safari Bogor
* Banded linsang (Prionodon linsang) privately owned
* Small Indian civet (Viverricula indica) privately owned
* Sulawesi palm civet (Macrogalidia musschenbroekii) at Taman Safari Bogor, no longer on display
* Sunda porcupine (Hystrix javanica) at Ragunan Zoo
* Western long-beaked echidna (Zaglossus bruijnii) at Batu Secret Zoo
* Java mouse-deer (Tragulus javanicus) at Taman Safari Bogor, no longer on display
* Sulawesi dwarf cuscus (Strigocuscus celebensis) at Taman Safari Bogor
* Black-spotted cuscus (Spilocuscus rufoniger) at Faunaland
* Grizzled tree-kangaroo (Dendrolagus inustus) at Taman Safari Bogor
* Spectral tarsier (Tarsius tarsier) at Faunaland
* Siau Island tarsier (Tarsius tumpara) at Ragunan Zoo
* Horsfield's tarsier (Cephalopachus bancanus) at Taman Safari Bogor, no longer on display
* Javan slow loris (Nycticebus javanicus) at a local bird market
* West Javan langur (Trachypithecus mauritius) at Taman Safari Bogor, no longer on display
* Black-crested Sumatran langur (Presbytis melalophos) at Taman Safari Bogor
* Javan surili (Presbytis comata) at Taman Safari Bogor
* Natuna Island surili (Presbytis natunae) at Ragunan Zoo
* Pagai Island macaque (Macaca pagensis) at Taman Safari Bogor, no longer on display
* Siberut macaque (Macaca siberu) at Taman Safari Bogor
* Heck's macaque (Macaca hecki) at Ragunan Zoo
* Gorontalo macaque (Macaca nigrescens) at Ragunan Zoo
* Muna-Buton macaque (Macaca ochreata brunnescens) at Ragunan Zoo, no longer on display
* Kloss’s gibbons (Hylobates klossii) at Taman Safari Bogor
* Müller's gibbon (Hylobates muelleri) at Ragunan Zoo
* Javan warty pig (Sus verrucosus) at Taman Safari Prigen
* Turkmenian kulan (Equus hemionus kulan) at Surabaya Zoo, no longer on display
* Sunda leopard cat (Prionailurus javanensis) at Faunaland
* Bay cat (Catopuma badia) at Taman Safari Bogor, no longer on display
* Sunda clouded leopard (Neofelis diardi) at Faunaland
Bird
* Javan banded pitta (Hydrornis guajanus) at a local bird market
* Javan kingfisher (Halcyon cyanoventris) at a local bird market
* Helmeted friarbird (Philemon buceroides) at a local bird market
* Greater coucal (Centropus sinensis) at a local bird market
* Large-billed crow (Corvus macrorhynchos) at a local bird market
* Sulawesi masked owl (Tyto rosenbergii) at Surabaya Zoo, no longer on display
* Barred eagle-owl (Bubo sumatranus) at Taman Safari Bogor
* Sumba hornbill (Rhyticeros everetti) at Eco Green Park
* Spotted kestrel (Falco moluccensis) at Taman Safari Bogor, no longer on display
* Papuan eagle (Harpyopsis novaeguineae) at Ragunan Zoo, no longer on display
* Blyth's hawk-eagle (Nisaetus alboniger) at Taman Safari Bogor, no longer on display
* Flores hawk-eagle (Nisaetus floris) at Ragunan Zoo, no longer on display
* Javan hawk-eagle (Nisaetus bartelsi) at Taman Mini Indonesia Indah
* Eastern cattle egret (Bubulcus coromandus) at Taman Mini Indonesia Indah
Reptile
* Kuhl's flying gecko (Gekko kuhli) at Jakarta Aquarium, no longer on display
* Earless monitor lizard (Lanthanotus borneensis) at Taman Mini Indonesia Indah
* Timor monitor (Varanus timorensis) at Taman Mini Indonesia Indah, no longer on display
* Golden-spotted tree monitor (Varanus boehmei) at Batu Secret Zoo, no longer on display
* Tricolor monitor (Varanus yuwonoi) at Taman Mini Indonesia Indah, no longer on display
* Peach-throated monitor (Varanus jobiensis) at Taman Mini Indonesia Indah
* Togian water monitor (Varanus togianus) at Batu Secret Zoo
* Sunbeam snake (Xenopeltis unicolor) privately owned
* Marine file snake (Acrochordus granulatus) at a reptile expo
* Halmahera python (Simalia tracyae) at Taman Mini Indonesia Indah
* Papuan olive python (Apodora papuana) at Taman Safari Bogor
* Southern whitelip python (Bothrochilus meridionalis) at Taman Mini Indonesia Indah, no longer on display
* White-lipped island pit viper (Trimeresurus insularis) at Batu Secret Zoo
* Wagler's pit viper (Tropidolaemus wagleri) at a reptile expo
* Flat-nosed pit viper (Trimeresurus puniceus) at Taman Safari Bogor, no longer on display
* Javan spitting cobra (Naja sputatrix) at Taman Mini Indonesia Indah
* Malayan pit viper (Calloselasma rhodostoma) at Taman Safari Bogor, no longer on display
* Sulawesi forest turtle (Leucocephalon yuwonoi) at Batu Secret Zoo
* Asian narrow-headed softshell turtle (Chitra chitra) privately owned
* Forsten's tortoise (Indotestudo forstenii) at Jakarta Aquarium
Fish
* Humpback puferfish (Pao palembangensis) at Taman Mini Indonesia Indah
* Barred soapfish (Diploprion bifasciatum) at Sea World Jakarta, no longer on display
* Javaen barb (Systomus rubripinnis) at Taman Mini Indonesia Indah, no longer on display
* New Guinea tandan (Neosilurus novaeguineae) at a local aquarium fish market
* Moustache catfish (Synodontis membranaceus) at Taman Mini Indonesia Indah
* Marble goby (Oxyeleotris marmorata) at a local fish store
* Freshwater moray eel (Gymnothorax polyuranodon) at Taman Mini Indonesia Indah
* Giant featherback (Chitala lopis) at a local fish store
* clubnose guitarfish (Glaucostegus thouin) at Sea World Jakarta, no longer on display