| Ailurops ursinus | Phalangeridae | Sulawesi | Kuskus beruang | Sulawesi bear cuscus |
| Axis kuhlii | Cervidae | Jawa Timur | Rusa bawean | Bawean deer |
| Babyrousa babyrussa | Suidae | Sulawesi | Babirusa | |
| Barbourula Borneoensis | Bombinatoridae | Kalimantan | Katak tanpa paru-paru | Bornean Flat-headed Frog |
| Bos javanicus | Bovidae | Jawa | Banteng jawa | |
| Bubalus depressicornis | Bovidae | Sulawesi | Anoa dataran rendah | |
| Bubalus quarlesi | Bovidae | Sulawesi | Anoa pegunungan | |
| Buceros bicornis | Bucerotidae | Kalimantan | Rangkong papan | |
| Callosciurrus adamsi | Sciuridae | Kalimantan | Bajing telinga botol | |
| Capricornis sumatraensis sumatraensis | Bovidae | Sumatra | Kambing hutan sumatra | |
| Casuarius bennetti | Casuariidae | Papua | Kasuari kerdil | Dwarf Cassowary |
| Casuarius unappendiculatus | Casuariidae | Papua | Kasuari gelambir tunggal |
| Catopuma badia | Felidae | Kalimantan | Kucing merah | Bay Cat |
| Cervus timorensis | Cervidae | Bali, Jawa and Timor | Rusa Timor | Javan Deer |
| Chelodina mccordi) | Chelidae | P. Roti, Nusa Tenggara Timur | Kura-kura leher ular | Roti Island snake-necked turtle |
| Chelonia mydas | Cheloniidae | Jawa | Penyu hijau | |
| Dendrolagus pulcherrimus | Macropodidae | Papua | Kanguru pohon mantel emas | Golden-mantled Tree-kangaroo |
| Dermochelys coriacea | Cheloniidae | Jawa | Penyu belimbing | |
| Dicerorhinus sumatrensis | Rhinocerotidae | Sumatra | Badak sumatra | Sumatran Rhinoceros |
| Eos cyanogenia | Psittacidae | Papua | Nuri Sayap Hitam | Black-winged Lory |
| Eretmochelys imbricata | Cheloniidae | Jawa | Penyu sisik | Hawksbill sea turtle |
| Hemiscyllium freycineti | Hemiscylliidae | Papua | Hiu karpet berbintik | Indonesian speckled carpetshark |
| Hylobates moloch | Hylobatidae | Jawa | Owa jawa | Silvery gibbon |
| Hylobates muelleri | Hylobatidae | Kalimantan | Owa-owa | Müller's Bornean gibbon |
| Hylobates syndactylus | Hylobatidae | Sumatra | Siamang | |
| Hystrix javanica | Hystricidae | Jawa | Landak jawa | Sunda Porcupine |
| Hystrix sumatrae | Hystricidae | Jawa | Landak sumatra |
| Lanthanotus borneensis | Scincidae | Kalimantan | Kadal coklat kalimantan | Earless monitor |
| Lariscus hosei | Sciuridae | Kalimantan | Bajing tanah | |
| Lepidochelys olivacea | Cheloniidae | Jawa | Penyu lekang | |
| Leptophryne cruentata | Bufonidae | Jawa Barat | Kodok darah | Bleeding toad |
| Leucopsar rothschildi | Sturnidae | Bali | Jalak Bali | |
| Macaca nigra | Cercopithecidae | Sulawesi Utara | Kera hitam sulawesi | Celebes crested macaque |
| Macaca pagensis | Cercopithecidae | Mentawai | Beruk mentawai | |
| Macrocephalon maleo | Megapodiidae | Sulawesi Tengah | Burung maleo | |
| Macrogalidia musschenbroekii | Viverridae | Sulawesi | Musang sulawesi | Sulawesi Palm Civet |
| Nasalis larvatus | Cercopithecidae | Kalimantan | Bekantan | |
| Neofelis diardi | Felidae | Sumatra dan Kalimantan | Macan dahan | Sunda Clouded Leopard |
| Nesolagus netscheri | Leporidae | Sumatra | Kelinci belang sumatra | Sumatran Striped Rabbit |
| Nycticebus javanicus | Lorisidae | Jawa | Kukang jawa | Javan slow loris |
| Orcaella brevirostris | Delphinidae | Kalimantan Timur | Pesut | Irrawaddy dolphin |
| Panthera pardus | Felidae | Jawa | Macan tutul jawa | |
| Panthera tigris sumatrae | Felidae | Sumatra | Harimau sumatra | |
| Paradisaea rubra | Paradisaeidae | Papua | Burung cendrawasih | |
| Phalanger alexandrae | Phalangeridae | Maluku Utara | Kuskus gebe | Gebe Cuscus |
| Phalanger matabiru | Phalangeridae | Maluku | Kuskus mata biru |
| Phalanger rothschildi | Phalangeridae | Maluku | Kuskus obi |
| Philautus jacobsoni | Phalangeridae | Jawa Tengah | Kodok pohon ungaran |
| Pongo abelli | Hominidae | Sumatra | Orang utan sumatra | |
| Pongo pygmaeus | Hominidae | Kalimantan | Orang utan kalimantan | |
| Presbytis comata | Cercopithecidae | Jawa | Surili | Javan surili |
| Presbytis frontata | Cercopithecidae | Kalimantan | Lutung dahi putih |
| Presbytis rubicunda | Cercopithecidae | Kalimantan | Lutung merah |
| Prionailurus bengalensis | Felidae | Jawa | Meong congkok | |
| Rhinoceros sondaicus | Rhinocerotidae | Jawa Barat | Badak jawa | |
| Scleropages formosus | Osteoglossidae | Sumatra | Arwana emas | Asian arowana |
| Simias concolor | Cercopithecidae | Mentawai | Monyet ekor babi | Pig-tailed langur |
| Strigocuscus celebensis | Phalangeridae | Sulawesi | Kuskus kerdil | Sulawesi Dwarf Cuscus |
| Sundasciurus juvencus | Sciuridae | Sumatra dan Bali | Bajing palawan | |
| Taphozous achates | Emballonuridae | Bali | Kelelawar berjenggot coklat | Indonesian Tomb Bat |
| Tarsius bancanus | Tarsiidae | Sumatra dan Kalimantan | Tarsius bangka | |
| Tarsius pelengensis | Tarsiidae | Sulawesi | Tarsius peleng | |
| Tarsius pumilus | Tarsiidae | Sulawesi | Tarsius pygmy | |
| Tarsius sangirensis | Tarsiidae | Sulawesi Utara | Tarsius sangir | |
| Tarsius tarsier | Tarsiidae | Sulawesi Utara | Tarsius sulawesi | |
| Thecurus crassispinis | Hystricidae | Kalimantan | Landak Borneo | Thick-spined bornean porcupine |
| Trachypithecus auratus | Cercopithecidae | Jawa | Lutung | |
| Tragulus javanicus | Tragulidae | Jawa | Kancil jawa | Java Mouse-deer |
| Tupaia chrysogaster | Tupaiidae | Mentawai | Tupai Mentawai | Golden-bellied Treeshrew |
| Varanus komodoensis | Varanidae | Nusa Tenggara | Komodo | Komodo dragon |
