The aeolid nudibranch Fiona pinnata (Eschscholtz, 1831) is an obligate rafter that occurs exclusively on macroalgal rafts and other floating substrata, and has a seemingly cosmopolitan marine distribution. Mitochondrial (mtDNA) and nuclear DNA sequence data were generated from specimens collected worldwide to test for global connectivity in this species. Phylogeographic analyses revealed three divergent mtDNA lineages, two of which were abundant and widespread. One of these lineages has an apparent circumequatorial distribution, whereas the other may have an antitropical distribution within the Pacific Ocean. Low genetic divergences within each lineage suggest that rafting can mediate dispersal across transoceanic scales. A third, highly divergent, lineage was detected in a single Indonesian specimen. Broadly concordant phylogeographic relationships were detected for the nuclear ITS1 region, with distinct tropical versus antitropical lineages observed. The substantial genetic divergences and largely allopatric distributions observed among the F. pinnata lineages suggest that they represent a species complex.