Life history traits (absence of larval phase, small size and hermaphroditism) do not predispose Amphipholis squamata to dispersal, yet paradoxically it has a nearly cosmopolitan distribution. Recent phylogenetic analyses of 16S mitochondrial DNA (mt-DNA) sequences revealed that (1) Amphipholis squamata is a complex of diverging clades, each of them being found in the North Atlantic as well as in the South Pacific Ocean, and (2) genetic structure is low along the coasts of New Zealand, leading the authors to conclude that rafting may allow important gene flow in this taxon and possibly worldwide distribution of species. For the present study, we obtained 16S mt-DNA sequences from individuals of the Mediterranean Sea, which we analysed along with published data. We show that several sub-clades of previously identified clades display an allopatric distribution, either Atlantic versus Mediterranean, or Mediterranean and Atlantic versus New Zealand. Furthermore, none of the haplotypes (from any sub-clade) have been found in both Mediterranean and Atlantic samples. These results establish that at least some species of the A. squamata complex, and possibly all of them, lack inter-oceanic or even Atlantic-Mediterranean distributions. We suggest that the worldwide distribution of some clades only reflects the antiquity of the clades, which are composed of several species.