ABSTRACT We re-assess the taxonomic status of Owenia Delle Chiaje, 1841 from Southern Brazil based on estuarine specimens from Paranaguá Bay (Paraná) and Babitonga Bay (Santa Catarina), and literature records. Owenia caissara sp. n. is diagnosed by a branchial crown with five pairs of tentacles, branched close to the base of the crown, rectilinear collar with a pronounced lateral slit, two ventrolateral ocelli partially covered by the collar, up to 23 hooks on a single row in the first abdominal segment, regularly curved nuchal shape, regularly moderate teeth curvature, and long and thin scales with oval transition. The description of Owenia caissara sp. n. reinforces the idea that Owenia fusiformis sensu lato is a complex of closely related species that can be distinguished on the basis of both macro- and micro- morphological traits.