The Sangihe Flying Snake was described in 1880 from a single specimen which was subsequently destroyed during World War II; it was originally described as a distinct species. This form was apparently restricted to the island of Sangihe, the largest of the Sangihe Islands, Indonesia (not Sulawesi as is often stated).
The snake reached a length of 1,4 m, it was bright green above and slightly paler below, parts of the head were yellowish colored. 
The status of this form is not known but it appears to be extinct.
 J. G. Fischer: Neue Amphibien und Reptilien. Archiv für Naturgeschichte 215-227. 1880
Depiction from: ‘J. G. Fischer: Neue Amphibien und Reptilien. Archiv für Naturgeschichte 46(1): 215-227. 1880′
This bird is known from several subfossil bones that were found during excavations on the island of Timor, Indonesia; it occurred on that island sympatrically with another buttonquail species, the Red-backed Buttonquail (Turnix maculosus (Temminck)) which is native to parts of Asia as well as Australia.
The remains were dated to an age of about 1372 to 1300 BP.
The Timor Buttonquail was larger than the other species and probably was endemic to the island or at least to the region, it is now clearly extinct. 
 Hanneke J. M. Meijer; Julien Louys; Sue O’Connor: First record of avian extinctions from the Late Pleistocene and Holocene of Timor Leste. Quaternary Science Reviews 203: 170-184. 2019
This species was described in 1849, it was endemic to the island of Java, Indonesia, an exact locality, however, appears to be unknown.
The shells reach sizes of about 2,3 cm in heigth, they are yellowish to olive with brown vertical flames and are sculptured with spiral lirae that are more prominent at the base of the body whorl. 
 Frank Kühler; Matthias Glaubrecht: Fallen into oblivion – the systematic affinities of the enigmatic Sulcospira Troschel, 1858 (Cerithioidea: Pachychilidae), a genus of viviparous freshwater gastropods from Java. The Nautilus 119: 15-26. 2005  Ristiyanti M. Marwoto; Nur R. Isnaningsih: The freshwater snail genus Sulcospira Troschel, 1857 from Java, with description of a new species from Tasikmalaya, west Java, Indonesia (Mollusca: Gastropoda: Pachychilidae). The Raffles Bulletin of Zoology 60(1): 1-10. 2012
The Siau Scops Owl is a highly threatened, very likely already extinct owl species that was endemic to the island of Siau north of Sulawesi, Indonesia; it is known only from the type specimen that had been collected in 1866.
The species reached a size of 17 cm.
The Siau Scops Owl is closely related to the Sulawesi Scops Owl (Otus manadensis (Quoy & Gaimard)) (see photo below) and was for some time considered a subspecies of it but is now regarded as a distinct species.
The Sumatran Black Bumblebee is known from a single specimen, a female that was collected (probably sometimes during the late 19th century) on the island of Sumatra, Indonesia.
The species has never been recorded since and might be extinct; however, it is also possible that the single existing specimen represents a melanistic individual of another species that simply has been mislabeled. 
 Paul H. Williams: An annotated checklist of bumble bees with an analysis of patterns of description (Hymenoptera: Apidae, Bombini). Bulletin of the Natural History Museum. Entomology series 67: 79-152. 1998
The Alor Giant Rat is known from subfossil remains that were recovered from cave deposits on the island of Alor in the Lesser Sundas, Indonesia.
The species was larger than most recent rat species and might have survived into quite recent times, the authors of the description in fact assume that it might be still alive today. 
 Julien Louys; Sue O’Connor; Mahirta; Pennilyn Higgins; Stuart Hawkins; Tim Maloney: New genus and species of giant rat from Alor Island, Indonesia. Journal of Asia-Pacific Biodiversity 11(4): 503-510. 2018
Emma’s Giant Rat was described in 1994, based on a single female specimen that had been cought in 1964, it apparently was endemic to the very small island of Owi, near Biak in the New Guinean part of Indonesia.
The species is believed to have mainly been arboreal, nothing else is known about its biology.
Martin’s Sulcospira Snail was described in 1898, it was apparently collected near Malangbon, a village (or now city) in central Java, Indonesia. 
The presumed type locality is now almost completely converted into rice fields, and the species, having not found since, is most likely extinct.
 Frank Kühler; Matthias Glaubrecht: Fallen into oblivion – the systematic affinities of the enigmatic Sulcospira Troschel, 1858 (Cerithioidea: Pachychilidae), a genus of viviparous freshwater gastropods from Java. The Nautilus 119: 15-26. 2005
The Great Kai Island Giant Rat was described in 1923, it is known from three specimens that had been collected on the island of Kai Besar in the New Guinean part of Indonesia.
The species reached a total length of about 36 cm including the relatively short tail.
The Great Kai Island Giant Rat is sometimes treated as a subspecies of the White-tailed Giant Rat (Uromys caudimaculatus (Krefft)) or is considered synonymous to the Aru White-tailed Giant Rat (Uromys caudimaculatus ssp. aruensis (Laurie & Hill)).
The Sangihe White-eye was described in 1888 based on a single specimen that was collected two years prior, it is, or maybe rather was, endemic to the island of Sangihe, Indonesia. This sole specimen was later thought to be lost but was rediscovered in 1990.
The species was later found out to be restricted to a tiny, higly threatened patch of remaining forest on this largely deforested island. As far as I know, the last confirmed record of this species was in February 1999, when a bird was heard singing, however, the bird itself was not seen. 
The Sangihe White-eye apparently now joins the ever-growing list of extinct species.
 P. C. Rasmussen; J. C. Wardill; F. R. Lambert; J. Riley: On the specific status of the sangihe White-eye Zosterops nehrkorni, and the taxonomy of the Black-crowned White-eye Z. atrifrons complex. Forktail 16: 69-80. 2000
The Sangihe Dwarf Kingfisher was described in 1898; it was for a long time treated as a subspecies of the Sulawesi Dwarf Kingfisher (Ceyx fallax (Schlegel)) (see depiction), a small, about 12 cm large, colorful bird that itself inhabits the island of Sulawesi, Indonesia. It is now considered a full species again.
The Sangihe Dwarf Kingfisher, as its name implies, is, or maybe was, restricted to the island of Sangihe Besar in the Sangihe Islands off northern Sulawesi.
The species differed from the Sulawesi Dwarf Kingfisher mainly by its slightly larger size as well as by its crown in which the blue bars are larger and more lustrous, by its blackish instead of lilac superciliary region and by its more lilac rump and wings. 
The Sangihe Dwarf Kingfisher was last seen in 1997, and given the fact that its home island is now almost completely deforested, the chances for any population to have survived until today are very low – it is possibly extinct.
Rueck’s Blue Flycatcher was described in 1881, it is so far known only from four specimens, two of which were collected at around 1917 or 1918 in the lowland forests of Sumatra, Indonesia while the other two are of doubtful origin.
The species reaches a length of about 17 cm, the males are bright dark blue on the upper side and have a white belly while the females are rufous brown.
Rueck’s Blue Flycatcher has not been found since the early 20th century and is most likely extinct.
Challenger’s Red-and-blue Lory (Eos histrio ssp. challengeri)
Challenger’s Red-and-blue Lory was restricted to the island of Miangas, northeast of Sulawesi, Indonesia, or from Nenusa Island. The subspecies, however, is known only from the type specimens and is not accepted by every ornithologist.
It differed from the other two subspecies by the lesser extent of the blue feathers, especially on the head.
The Red-and-blue Lory still exists on three of the Talaud Islands, Indonesia where an endemic subspecies, the Talaud Red-and-blue Lory (Eos histrio ssp. talautensis Meyer & Wiglesworth), occurs.
This species was described in 1940 based on a single specimen that had been found in the 1920s on the island of Pulau Enggano, western Indonesia.
The species is, or rather was, living sympatrically with two additional congeneric species: the endemic and critically endangered Enggano Rat (Rattus enganus (Miller)) as well as the rather widespread Malayan Wood Rat (Rattus tiomanicus (Miller)).
This up to now unnamed mouse species is known from subfossil remains that were recovered, together with the remains of a second congeneric but larger species, from cave deposits on the island of Timor.
 Ian Glover: Archaeology in eastern Timor, 1966-67. Department of Prehistory, Australian Naitonal Univ 1986  Samuel T. Turvey: Holocene Extinctions. Oxford University Press, USA 2009
Elephants are probably among the best known animals, animals that in the general public may possibly not be mistaken for something else – yet in a scientifically sense elephants are quite uninvestigated and many questions remain open.
One of these questions is how many subspecies actually exist.
Asian elephants inhabit the Indian subcontinent, the islands of Sri Lanka, Sumatra, and Borneo, each place is inhabited by an endemic subspecies respectively. The species was much more widespread in the past.
The animals are still occasionally kept in captivity as work elephants, even more so in the past, thus many ‘wild’ elephant populations, living or extinct, may in fact just represent feral populations.
The extinct elephant population from the island of Java obviously was a native one, since elephants are known to have lived on the island at least since the last interglacial.
Like in other places in Asia also the Javan Elephants were occasionally kept in captivity, whence they were shipped from place to place across the islands in the Sulu sea many hundreds of years ago, usually as much-valued gifts between rulers. In about 1395 for example, the Raja of Java gave two elephants to the Raja of the Sultanate of Sulu (this Sultanate comprised parts of Mindanao and Palawan, Philippines as well as north-eastern Borneo). Some of the descendants of these elephants were subsequently released on the island of Borneo.
The wild Javan elephant population died out soon after, but their descendants obviously survive on the island of Borneo, at least genetically imbedded within the endemic Bornean Elephant population, which was described as a distinct subspecies (Elephas maximus ssp. borneensis P. E. P. Deraniyagala) in 1950. 
The Java Elephant was once described as Elephas maximus ssp. sondaicus P. E. P. Deraniyagala on the basis of an illustration of a carving on Borabudur, a 9th-century Mahayana Buddhist temple in Magelang, Central Java, this name, however, seems to be invalid. Nevertheless the native Javan Elephant population appears to have been distinct from the other populations and most probably represented an now extinct endemic subspecies.
The youngest Java Elephant remains can be dated to about 1350. 
The island of Java obviously harbored another elephant species, which was described in 1908 as Elephas hysudrindicus Dubois, it is known from the Pleistocene and should not be mistaken for the recently extinct Javan Elephant.
 Earl of Cranbrook; J. Payne; Charles M. U. Leh: Origin of the elephants Elephas maximus L. of Borneo. Sarawak Museum Journal 2008