China is a hotspot for species’ discovery nowadays and harbours some of the most threatened environments in the world due to human activities. Here we describe a new remarkable gastropod species from an ancient freshwater lake in Yunnan, south-west China, Squamapex taiji gen. et sp. nov. within a new monospecific family of Truncatelloidea, Squamapicidae fam. nov.. The highly ornamented protoconch of Squamapicidae, with a microstructure distinct from that of the teleoconch, has rarely been found in true freshwater gastropods, being previously mostly known from marine or migratory gastropods with veliger larvae. The most complete family-level and first-dated phylogeny of Truncatelloidea, the largest and most diverse superfamily within Mollusca, based on two mitochondrial and three nuclear markers, shows that Squamapicidae belong to a distinct ancient lineage with Cretaceous origin. Its sister-group, unique protoconch, and distribution suggest a Tethys Ocean origin of this new family.