Wurm et al. (1975) classified the AP languages as members of the putative Trans-New Guinea Phylum.

[4] However, the authors offered little evidence for this classification and remained somewhat doubtful, noting, “whichever way they [the Timor–Alor–Pantar languages] are classified, they contain strong substratum elements of the other … phyla involved” (Wurm et al. 1975:318).

Bottom-up reconstruction based on regular sound correspondences may shed further light on these issues.

A 2019 phylogenetic study of Alor-Pantar by Kaiping and Klamer gives the following internal structure:[7] Kaiping and Klamer (2019b) have found that the four major Alor–Pantar subgroups, namely Pantar, Blagar, Central Alor, and East Alor, form different phylogenetic trees depending on the methodology that is applied.

Language documentation efforts in the early 21st century have produced a range of published documentary materials.