The North Halmahera languages are classified by some to be part of a larger West Papuan family, along with the languages of the Bird's Head region of Western New Guinea, while others consider North Halmahera to form a distinct language family, with no demonstrable relationship outside the region. The languages of North Halmahera appear to have the closest affinity with the languages of the Bird's Head, which suggests a migration from the western Bird's Head to northern Halmahera. However, Ger Reesink notes that the evidence for genetic relatedness between the different "West Papuan" groupings is too skimpy to form a firm conclusion, suggesting that they be considered an areal network of unrelated linguistic families. Moreover, many speakers of North Halmahera languages, such as the,, and peoples, are physically distinct from New Guineans, while Papuan traits are more prevalent among the Austronesian-speaking peoples of South Halmahera. Robert Blust considers this paradox to be a result of historical language replacement. Ternate, Tidore, West Makian, and Sahu have received extensive Austronesian influence in terms of grammar. Bert Voorhoeve noted a set of lexical similarities between the North Halmahera languages and the Central Papuan languages of the south coast of Papua New Guinea, possibly arising from potential language contact.
Internal classification
The family is dialectally heterogeneous, with blurry lines between different languages. While different authors tend to disagree on the number of distinct languages identified, there is general accord regarding the internal subgrouping of the family. The classification used here is that of Voorhoeve 1988. West Makian is divergent due to heavy Austronesian influence. It was once classified as an Austronesian language. It should be distinguished from East Makian, an unrelated Austronesian language. There is a degree of mutual intelligibility between the Galela–Tobelo languages, and Voorhoeve 1988 considered them dialects of a language he called Northeast Halmaheran, though most speakers consider them to be distinct languages. Ternate and Tidore are generally treated as separate languages, though there is little Abstand involved, and the separation appears to be based on sociopolitical grounds. Voorhoeve groups these idioms together as varieties of a unitary "Ternate-Tidore" language, while Miriam van Staden classifies them as distinct languages. Other North Halmahera languages, such as Galela and Tobelo, have received significant influence from Ternate, a historical legacy of the dominance of the Ternate Sultanate in the Moluccas. Many Ternate loanwords can be found in Sahu.
Proto-language
Proto-North Halmahera consonants are : Proto-North Halmahera is notable for having the voiced retroflex stop *ɖ, as retroflex consonants are often not found in Papuan languages. The following proto-North Halmahera reconstructions are listed in Holton and Klamer. Most of the forms in Holton and Klamer are derived from Wada. ;proto-North Halmahera reconstructions
