Genetic distances among strains of P. sexaurelia were compared by sequencing the mitochondrial cytochrome b gene. The relationships of P. sexaurelia with representative strains of other species of the P. aurelia complex and related species, i.e. P. schewiakoffi, P. jenningsi and P. multimicronucleatum were evaluated. All investigated P. sexaurelia and P. dodecaurelia strains grouped together with high support. This P. sexaurelia/P. dodecaurelia cluster was furthermore composed of three distinct, strongly supported subgroups. Two of these groups contained both P. sexaurelia and P. dodecaurelia strains, suggesting that these species are not monophyletic. The third branch was composed of strains from Sevilla, Spain and was deeply separated (12-14 % p-distance) from the other P. sexaurelia/P. dodecaurelia clades. This illustrates the urgent need for further work and more intense sampling of these "rare" species, in order to understand the status and the relationships of P. sexaurelia and P. dodecaurelia within the P. aurelia species complex. We recommend that general investigations on the speciation process be conducted within and between species of the P. aurelia complex due to the high genetic variation combined with observations that for some of the species possible cryptic speciation may have occurred. This is emphasized by data showing that for some species within this complex, species status may be less static and more dynamic than originally thought.