Abstract: Abstract This paper refines the subgroupings of the Timor-Alor-Pantar (TAP) family of Papuan languages, using a systematic Bayesian phylogenetics study. While recent work indicates that the TAP family comprises a Timor (T) branch and an Alor-Pantar (AP) branch (Holton et al., 2012; Schapper et al., 2017), the internal structure of the AP branch has proven to be a challenging issue, and earlier studies leave large gaps in our understanding. Our Bayesian inference study is based on an extensive set of TAP lexical data from the online LexiRumah database (Kaiping et al., 2019b; Kaiping and Klamer, 2018). Systematically comparing different analytical models and tying them back to the evidence in terms of historical linguistics, we arrive at a subgrouping structure of the TAP family that is based on features of the phylogenies shared across the different analyses. Our TAP tree differs from all earlier proposals by inferring the East Alor subgroup as an early split-off from all other AP languages, instead of the most deeply embedded subgroup inside that branch. The evidences suggests that dialect cluster effects played a major role in the formation of today’s Timor-Alor-Pantar languages.