• adenine nucleotide transporter (ANT) intron;
  • Ascidiacea;
  • cytochrome c oxidase subunit I (COI);
  • phylogeny;
  • Pyuridae

Cryptic diversity represents a major challenge to the accurate assessment of biodiversity, but the combined use of genetic and morphological analyses has proven to be a powerful approach to detect it. This is especially important for groups for which genetic information is not yet available. Here, we studied the highly conspicuous habitat-forming Pyura stolonifera species complex (Tunicata), which, as has recently been revealed, shows surprising levels of cryptic diversity, but whose systematics and biogeographical patterns in Australasia nonetheless remain poorly understood. We first present detailed taxonomic information of all the species associated with the P. stolonifera species complex. We then proceed to describe the results of an exhaustive survey that included south-east Australia, Tasmania, and New Zealand. Subsequently, we present morphological and mitonuclear genetic analysis of two unresolved lineages that comprise the species Pyura praeputialis and a species that is formally described here (Pyura doppelgangera sp. nov.). Although the ranges of these two species overlap on mainland Australia, we found no sites at which both species live in sympatry, and there was no morphological or genetic evidence of hybridization. Taken together, the present study illustrates the usefulness of a combined morphogenetic approach in unravelling overlooked marine diversity in a relatively well-studied region. © 2013 The Linnean Society of London