The Babyloniidae is a family of marine snails consisting of 21 species and two genera. Current taxonomic debates on the Babyloniidae are mainly due to their extremely similar shell morphologies, which have led to incorrect locality records and mislabelling in legal or illegal international trade. We have therefore constructed a phylogeny of the Babyloniidae with high species coverage (57% of the family) by using multi‐locus genes (cytochrome c oxidase subunit I [COI], 16S, and H3) with four species delimitation methods (Best Close Match [BCM], Assemble Species by Automatic Partitioning [ASAP], Bayesian Poisson Tree Process [bPTP] and Multi‐rate Poisson Tree Processes [mPTP]). Based on our results, 13 clades/operational taxonomic unit were observed, which confirms pre‐existing species status for 10 Babylonia and one Zemiropsis taxa: B. areolata (Link, 1807), B. borneensis (Sowerby II, 1864), B. feicheni Shikama, 1973, B. formosae (Sowerby II, 1866), B. japonica (Reeve, 1842), B. lutosa (Lamarck, 1816), B. pieroangelai Cossignani, 2008, B. spirata (Linnaeus, 1758), B. valentiana (Swainson, 1822), B. zeylanica (Bruguière, 1789) and Z. papillaris (Sowerby I, 1825). A monophyletic group with four species collected from Indonesia which includes B. spirata f. balinensis Cossignani, 2009, B. spirata f. semipicta (Sowerby II, 1866) and B. angusta Altena & Gittenberger, 1981, implying they should belong to a single species, B. semipicta. Additionally, we suggest B. formosae habei Altena & Gittenberger, 1981 should be escalated as B. habei, and not as a subspecies.