The Peba–Yaguan language family is located in the northwestern Amazon, but today Yagua is the only remaining spoken language of the family.
Munichi is an extinct language which was spoken in the village of Munichis, about 10 miles (16 km) west of Yurimaguas, Loreto Region, Peru. In 1988, there were two mother-tongue speakers, but they had not met since the 1970s. The last known fluent speaker, Victoria Huancho Icahuate, died in the late 1990s. As of 2009 there were several semi-speakers who retained significant lexical, and partial grammatical, knowledge of the language.
The Waorani (Huaorani) language, commonly known as Sabela is a vulnerable language isolate spoken by the Waorani people, an indigenous group living in the Amazon rainforest between the Napo and Curaray Rivers in Ecuador. A small number of speakers with so-called uncontacted groups may live in Peru.
The Chicham languages, also known as Jivaroan is a small language family of northern Peru and eastern Ecuador.
Puquina is a small, putative language family, often portrayed as a language isolate, which consists of the extinct Puquina language and Kallawaya, although it is assumed that the latter is just a remnant of the former mixed with Quechuan. Puquina speakers are last mentioned in the early nineteenth century.
The Cahuapanan languages are a language family spoken in the Amazon basin of northern Peru. They include two languages, Chayahuita and Jebero, which are spoken by more than 11,300 people. Chayahuita is spoken by most of that number, but Jebero is almost extinct.
Itonama is a moribund language isolate once spoken by the Itonama people in the Amazonian lowlands of north-eastern Bolivia. It was spoken on the Itonomas River and Lake in Beni Department.
Kunza is a mostly extinct language isolate spoken in the Atacama Desert of northern Chile and southern Peru by the Atacama people, who have since shifted to Spanish. The last speaker was documented in 1949; however, it has since been learned that the language is still spoken in the desert.
Omurano is an unclassified language from Peru. It is also known as Humurana, Roamaina, Numurana, Umurano, and Mayna. The language was presumed to have become extinct by 1958, but in 2011 a rememberer was found who knew some 20 words in Omurano; he claimed that there were still people who could speak it.
Andaqui is an extinct language from the southern highlands of Colombia. It has been linked to the Paezan or Barbacoan languages, but no connections have been demonstrated. It was spoken by the Andaqui people of Colombia.
The Mascoian languages, also known as Enlhet–Enenlhet, Lengua–Mascoy, or Chaco languages, are a small, closely related language family of Paraguay.
Macro-Warpean is a provisional proposal by Kaufman (1994) that connected the extinct Huarpe language with the previously connected Muran and Matanawí (Mura–Matanawí). Morris Swadesh had included Huarpe in his Macro-Jibaro proposal.
The extinct Hibito–Cholón or Cholónan languages form a proposed language family that links two languages of Peru, Hibito and Cholón. This family was believed to be extinct but in 2021 a native speaker was rediscovered, she is Martha Pérez Valderrama, she is currently the only known speaker of this family. They may also be related to the extinct Culle language, and perhaps to the language of the Chachapoya, but the data for all of these languages is poor.
Guató is a possible language isolate spoken by 1% of the Guató people of Brazil.
The Monde languages of Brazil form a branch of the Tupian language family.
Tequiraca (Tekiráka), also known as Abishira, Aiwa, Ixignor, or Vacacocha, is an extinct language once spoken in Peru. In 1925 there were between 50 and 80 speakers in Puerto Elvira on Lake Vacacocha. It is presumed extinct some time in the mid 20th century, though in 2008 two rememberers were found and 160 words and short sentences were recorded. Today, most ethnic Aiwa people have shifted to Kichwa and Spanish.
The Ofayé or Opaye language, also Ofaié-Xavante, Opaié-Shavante, forms its own branch of the Macro-Jê languages. It is spoken by only a couple of the small Ofayé people, though language revitalization efforts are underway. Grammatical descriptions have been made by the Pankararú linguist Maria das Dores de Oliveira (Pankararu), as well as by Sarah C. Gudschinsky and Jennifer E. da Silva, from the Universidade Federal do Mato Grosso do Sul.
Taushiro, also known as Pinche or Pinchi, is a nearly extinct possible language isolate of the Peruvian Amazon near Ecuador. In 2000 SIL counted one speaker in an ethnic population of 20. Documentation was done in the mid-1970s by Neftalí Alicea. The last living speaker of Taushiro, Amadeo García García, was profiled in The New York Times in 2017.
The Tiniwan languages are two extinct and one moribund language of Colombia that form a small family.
The Timotean languages were spoken in the Venezuelan Andes around what is now Mérida. It is assumed that they are extinct. However, Timote may survive in the so-far unattested Mutú (Loco) language, as this occupies a mountain village (Mutús) within the old Timote state.
