This article is an analysis of the genetic relationship between Stoney and Assiniboine and documents Assiniboine’s major dialectal division in the light of comparative and historical data. The first objective consists in a critical analysis of the widespread assumption—which is based on lexicostatistics, sound changes, and lexical differentiation—that Stoney separated from the Dakotan group independently from Assiniboine. I show that many of the sound changes and lexical differences found in Stoney are shallow diachronically and cannot be used to sustain an early separation hypothesis. On the contrary, there are a number of shared innovations that indicate Stoney and Assiniboine descend from an immediate common ancestor, Proto-Nakoda. The second objective is to provide new data on Assiniboine dialectal divisions—specifically phonological reshaping of stems—that help clarify and further refine the internal dialectal divisions of Assiniboine and its historical and genetic relationships with Stoney.