The term Papuan languages refers to those languages of the western Pacific which are neither Austronesian nor Australian. The majority of the Papuan languages are spoken on the island of New Guinea (which is divided between the countries of Papua New Guinea and Indonesia), with a few spoken in the Solomon Islands, and a number in various islands of Indonesia, in particular Halmahera, Timor, Alor and Pantar . One Papuan language is spoken in Australia, in the eastern Torres Straits.

From the above it can be seen that the term 'Papuan Languages' is not meant to imply any unity. As described below, there is a great deal of diversity amongst the Papuan languages and it has not yet been shown that they are all related. In fact, they fall into a large number of family groupings.

Although there has been relatively little study of the Papuan languages, compared with, say, Australian or Austronesian languages, a number of distinct genetic groups have been identified by linguists. In the field of Papuan linguistics these genetic groups are referred to as phyla. The largest phylum posited for the Papuan region is the Trans-New Guinea phylum, consisting of a large number of languages running mainly along the highlands of New Guinea, from the Indonesian province of Irian Jaya (the western half of the island) through to Papua New Guinea (the eastern half).

One commonly-used classification system for Papuan language phyla is listed below, with the number of languages in each phylum in parentheses. The list also incudes isolate languages, for which no genetic affiliation is known. This scheme is that used by the Ethnologue, based on the work of linguist S.A. Wurm and others. Other linguists, including William A. Foley, have identified over sixty language families, suggesting that the grouping of certain languages into phyla by earlier linguists may have been based on structural or other similarities, which may or may not indicate genetic relationships. Since perhaps only a quarter of Papuan languages have been studied in detail, linguists' understanding of the relationships between them will likely continue to be revised.

• Abinomn language (isolate)
• Amto-Musan languages (2)
• Bayono-Awbono languages (2)
• Burmeso language (isolate)
• Busa language (islolate)
• East Bird's Head languages (3)
• East Papuan languages (36)
• Geelvink Bay languages (33)
• Guahiban languages (5)
• Karkar-Yuri language (isolate)
• Kibiri language (isolate)
• Kwomtari-Baibai languages (6)
• Left May languages (7)
• Lower Mamberamo languages (2)
• Sepik-Ramu languages (104)
• Sko languages (7)
• Torricelli languages (48)
• Trans-New Guinea languages (552)
• West Papuan languages (26)
• Yale language (isolate)

There are also many Austronesian languages spoken in New Guinea