The mountainous Gorny Altai in southern Siberia constitutes the western part of the Altai–Sayan Folded Belt in the northwestern part of the Central Asian orogenic belt, which contains precious records of the lost major Proterozoic–Paleozoic ocean called the Paleo-Asian Ocean (PAO). This paper briefly introduces the latest microfossil (radiolarian and conodont) information recovered from the Lower Paleozoic siliceous and carbonate sequences of the Gorny Altai. The fossils of planktonic biota inhabited in PAO range back to the early Cambrian, in which the world's oldest radiolarians are included. In addition, numerous well-preserved conodonts as well as graptolites were recovered from Cambrian, Ordovician, and Silurian strata in the Gorny Altai. These recorded the Early Paleozoic biodiversity and their secular change both in pelagic and continental margin settings within PAO.