Fossiliferous Upper Vendian strata are discovered in the Upper Proterozoic to Lower Paleozoic Fore-Yenisei sedimentary basin under a thick Mesozoic–Cenozoic cover in southeastern West Siberia. Two depositional systems are recognized based on sedimentological features: (1) wave- and current-agitated shoreface–forereef–biohermal reef system (Vostok-3 Borehole section) and (2) tidal flat–evaporite basin (Averinskaya-150 Borehole section). The forereef facies yielded fossilized tubular calcareous skeletons of reef-building metazoans Cloudina riemkeae, Cloudina hartmannae and Cloudina carinata, phosphatized Namacalathus-like fossils, and a diversity of tubular phosphatized and agglutinated tubular fossils. The fossil assemblage can be interpreted as the evidence of ecological complexity of the reef system. Paleontological characteristics suggest correlation of the Vendian strata with the lowermost Purella antiqua Assemblage Zone and the boundary interval with the underlying Anabarites trisulcatus Assemblage Zone of the Siberian Platform. Therefore, at least in the late Proterozoic, the Fore-Yenisei sedimentary basin was part of a larger pericratonic depositional system on the western margin of the Siberian Craton.