Species that disperse by means of planktonic larvae are typically not genetically structured along environmentally homogeneous coastlines. In contrast, those that lack a planktonic dispersal phase, or species with a short (<12 h) pelagic propagule duration (PPD), tend to show population genetic structure at small spatial scales, with dispersal often taking place by means of a stepping-stone process. These general patterns emerged in the literature after decades of studies based on relatively poorly resolving genetic markers (e.g. allozymes and DNA sequences). However, recent evidence based on more informative genetic markers (microsatellites) suggests that stepping-stone dispersal is not uncommon in species with a PPD of days to weeks. Here, we used microsatellite data to investigate genetic structure in a non-native population of the solitary ascidian Pyura doppelgangera in southern Australia. This species is part of a group of marine invertebrates with great potential to become invasive, whose 1 day PPD was considered to be sufficiently long to drive genetic homogeneity along continuous coastlines. We identified genetic structure at scales of a few kilometres, with clear signatures of larval retention at natal sites. This limited dispersal potential may explain why the species has not yet established itself throughout the invaded region. Our results add to the growing evidence that many previous studies may have over-interpreted the dispersal potential of this group, likely because of insufficient resolution of the more slowly evolving DNA markers used to make inferences at ecological time-scales.