Based on some coincident morphological characters and distribution, it was believed for a long time that Mica micula was the post-larval stage of a species of Bargmannia, a genus having a very wide geographic distribution. Recent studies, however, have shown that it is much more likely to be the post-larval form of the physonect Pyrostephos vanhoeffeni, which is very common in both Antarctic and sub-Antarctic waters. Until now, molecular evidence to support this theory has been lacking. In the present study 34 nectophores of P. vanhoeffeni and four colonies of M. micula collected from three areas in the Southern Ocean were analysed for the 16S rRNA gene. Five haplotypes were identified, which formed two clearly distinct lineages. Three haplotypes were found exclusively in Admiralty Bay and were shared between individuals of both studied taxa, confirming that M. micula is indeed the post-larval stage of P. vanhoeffeni. Two additional haplotypes were found in one open ocean locality and in Admiralty Bay.