The Sinu Parakeet was described in 1917; it is restricted to the dry forests of the Sinú Valley in northern Colombia; it was considered a subspecies of the Painted Parakeet (Pyrrhura picta (Müller)) but is now known to be a distinct species. 
The species has not been seen since the 1940s and is most likely extinct.
 Stuart H. M. Butchart; Stephen Lowe; Rob W. Martin; Andy Symes; James R. S. Westrip; Hannah Wheatley: Which bird species have gone extinct? A novel quantitative classification approach. Biological Conservation 227: 9-18. 2018
The Paraguas Rain Frog was described in 1996 when it probably was already extinct, it is known only from a single site, a stream in Alto de Oso on the western flank of the Cordillera Occidental in the Chocó Department of Colombia.
The species has not been recorded since 1986, despite several surveys, and is probably extinct.
This species was described in 1862, it is apaprently known from two populations in the Department of Antioquia, Colombia, according to other sources, however, it is known from only a single locality in Tolima south of Antioquia.
The tree was locally known as Achote cimarrón or Zapotillo.
This species was described in 2011 and was originally known only from the type, a subadult individual that had been collected in 1979 in a fragment of moist forest on the western slopes of the Ecuadorian Andes.
A second specimen, discovered some years later in a museum collection was collected in 1959 at La Guayacana in western Colombia.
The Small Whiskered Bat apparently is/was restricted to the so-called Chocó ecoregion, lowland forest areas that now are mostly deforested, and is probably extinct. 
 Ricardo Moratelli; Don E. Wilson: A second record of Myotis diminutus (Chiroptera: Vespertilionidae): its bearing on the taxonomy of the species and discrimination from M. nigricans. Proceedings of the Biological Society of Washington 127(4): 533-543. 2015
The Lake Tota Feeler Fish is known from only ten specimens that were caught between 1942 and 1957 in the Lake Tota and is now considered extinct.
This about 14 cm long, incredibly ugly fish is unique among Pencil Catfishes in possessing remarkable rings of extensive adipose tissues surrounding its body, and giving it a somewhat large intestine-like appearance.
So far, nothing is known about its biology, the extinction was probably caused on the one hand by the introduction of the Rainbow Trout (Oncorhynchus mykiss (Walbaum)), and on the other hand by the subsidence of the water level due to seismic activities.
 Scott A. Schaefer; Luis Fernández: Redescription of the Pez Graso, Rhizosomichthys totae (Trichomycteridae), of Lago de Tota, Colombia, and Aspects of Cranial Osteology Revealed by Microtomography. Copeia 2009(3): 510-522. 2009
Kress’s Chlorospatha was described in 1991, it is known only from the type locality, a small enclave of relatively intact, lowland primary forest southeast of the town of Quibdó in the Chocó Department of Colombia, where the plants grew on slopes near a stream in deep primary forest. 
The species was collected in 1986, at a time when extensive logging began in the region; the type locality is now apparently completely deforested and this species seems to be extinct.
 Michael H. Grayum: Chlorospatha kressii (Araceae), a new compound-leved species from Chocó Department, Colombia. Novon 1(1): 12-14. 1991
The Black-hooded Thrush (Turdus olivater (Lafresnaye)) (see photo) occurs in northern South America, Mainly in Colombia and Venezuela, eight subspecies are distinguished of which the one, discussed here, is endemic to the Cauca Vvalley in southwest Colombia.
The habitat of the Cauca Black-hooded Thrush is now more or less completely destroyed by logging and this little known subspecies is possibly extinct.
The Pintail inhabits large parts of South America, two or three subspecies are recognized.
The extinct subspecies discussed here, Niceforo’s Pintail, once inhabited the higher altitude regions of Colombia. The birds, which reached a length of 61 to 71 cm, were first described as a distinct form in the year 1940.
The local duck-hunters, however, already knew them for a much longer time, they called the birds Pato Pico de Oro de Colombia resp. Pato Pico de Oro de Nicéforo, and studiously hunted them, and finally managed to extirpate the whole population within the next 12 years.
The last birds were seen in the year 1952 (or 1956, according to other sources).
 Steve Madge; Hilary Burn: Waterfowl: An identification guide to the Ducks, Geese and Swans of the World. Houghton Mifflin, Boston 1988
The Angelito Stub-foot Toad was described in 1998; it is known from two localities, one in Colombia and the other one in northern Ecuador (only based on museum specimens).
The species is beautifully green colored with a rather yellowish green under side.
The Angelito Stub-foot Toad was already nearly extinct when it was described and only few specimens were found; it was last recorded in 2000 and appears to be extinct now.
 Luis A. Coloma; William E. Duellman; Ana Almendáriz C.; Santiago R. Ron; Anrea Terán-Valdez; Juan M. Guayasamin: Five new (extinct?) species of Atelopus (Anura: Bufonidae) from Andean Colombia, Ecuador, and Peru.
The Bearded Tachuri (see depiction) is distributed over many parts of northern South America, the subspecies discussed here, hoevere is higly localized and does only occur in the Sabanas de Bogotá in the Department of Cundinamarca in central Colombia.
This species, a small reddish brown frog, was described in 1982, it is known only from three specimens.
The Sonson Frog was found near Sonsón, a municipality in the Cordillera Central, in the Department of Antioquia, Colombia. The species inhabited wet rocks near a stream in primary forest at an elevation of about 2780 m, this locality, however, is now highly degraded due to guerilla activities.
The Sonson Frog was never found again since its description and is very likely extinct.