To assess the sources of population differentiation in Late Bronze Age Western Siberia, measurements of 68 cranial samples of this and earlier periods were processed with multivariate statistical methods. Results support the idea of at least two post-Afanasyevo migrations to Siberia from the west—pre-Andronovo and Andronovo. The former was represented by Chaa-Khol, Yelunino, and Samus people. Those associated with Karakol culture partly resemble the above and partly both autochthonous populations—that of Baraba (“Northern Eurasian formation”) and that of Okunev culture (“Southern Eurasian formation”), which appear to be two extremes of a single continuum. Differences between the two Andronovo traditions, Fedorovka and Alakul, are likely due to the local substratum in the former rather than to various origins. The Karasuk group arose through admixture between Okunev and Andronovo. People associated with the classic Karasuk culture are closer to the former, while those of the Kamenny Log stage tend toward the latter. People of the Upper Irtysh and the Mongun-Taiga people from Baidag III resemble those of Karasuk. Two pooled groups, Irmen and Mongun-Taiga, and the Pakhomovskaya sample indicate a possible admixture between both autochthonous formations, Northern and Southern, as well as Andronovo and Karasuk. Among the so-called Andronoid groups, only Yelovka and Pakhomovskaya, as well as a sample from Yelovka I, suggest admixture between Andronovans and Western Siberian natives, while Cherkaskul and Korchazhka, like the Late Krotovo groups from Sopka and Cherno-Ozerye and the Begazy-Dandybai group of Baraba, deviate from the Northern Eurasian formation toward Okunev rather than Andronovo. Among the two Eurasian formations, the Southern one (i.e., Okunev) was more affected by admixture between the autochthones and the immigrants.