The well-known ciliate, Mesodinium Stein, 1863, is of great importance to marinemicrobial food webs and is related to the "red tides". However, it is possibly one of the mostconfusing ciliate taxa in terms of its systematic position: either the morphologicalor the molecular data excluded it from all the other known assemblages or groups.In the current work, the sequences of small subunit ribosomal RNA (SSU rRNA) genesfor all isolates available are analysed and an examination of the secondary structurepatterns of related groups is carried out. The results indicate that (1) Mesodinium invariably represents a completely separated and isolated clade positionedbetween two subphyla of ciliates with very deep branching, which indicates thatthey should be a primitive or ancestral group for the subphylum Intramacronucleata;(2) the secondary structure of the SSU rRNA of Mesodinium species is unusual in that, while the secondary structureof V4 in Mesodinium sp. has the deletionscommon to all litostome ciliates, it has more extensive deletions in helix E23_8and a longer helix E23_1; (3) combiningthe phylogenetic and morphological information, we suggest establishing Mesodiniea cl. nov. , including the order MesodiniidaGrain, 1994, belonging to the subphylum Intramacronucleata.