Bora and Muinane are two neighboring, relatively closely related languages spoken in the North-West Amazon. Whether these two languages can be shown to be genealogically related to other languages is still debated. In this paper, we provide a reconstruction of 416 proto Bora-Muinane word forms and of the proto Bora-Muinane phonological system. Our reconstruction confirms an earlier reconstruction by Aschmann (1993), but also differs from it in some important respects. We firmly establish sound changes in Bora and Muinane based on extensive data and first-hand knowledge of the languages involved. The reconstructed proto Bora-Muinane forms presented here provide a sound basis for re-evaluating the genealogical relationship of Bora-Muinane with Witoto and Ocaina, which was proposed by Aschmann (1993), and opens the possibility to search for genealogical relations with other languages.