The term Myzozoa superseded the previous term "Miozoa", by the same authority, and gave a slightly altered meaning.
Within Myzozoa, there are around six subphyla:
- Apicomplexa – parasitic protozoa that lack axonemal locomotive structures except in gametes
- Chromerida – a marine phylum of photosynthetic protozoa
- Dinoflagellates – mostly marine flagellates many of which have chloroplasts
It should be noted that the term/group Myzozoa was not considered in a recent resolution of protist groups. Strict taxonomy only considers common traits possessed by all organisms of the group. Some organisms within each of the component groups of Myzozoa have lost the ability for Myzocytosis. Further, as taxonomy pays no account of molecular phylogeny, one current classification has all alveolate taxa other than dinoflagellates, ciliates and dinoflagellates, named under the grab bag term "Protalveolata". The difficulty of placing very early dinoflagellates either within or outside the group "dinoflagellates" continues to favour classifications such as Protalveolata, as does the potential polyphyly between the two genera of "colpodellids" Voromonas and Colpodella.
The most closely related large clade to the myzozoans are the ciliates. Both of these groups of organisms — unlike the majority of eukaryotes studied to date — seem to have a linear mitochondrial genome. Most other eukaryotes that have had their mitochondrial genomes examined have circular genomes. However, the taxonomic term Myzozoa specifically excludes ciliates which are rather under the higher taxonomic rank Alveolata. Thus, Alveoata includes two large groups: Myzozoa and Ciliophora  plus the smaller groups discussed above.
The branching order within both Myzozoa and Protalveolata, is only partly understood. Three groups - the Colpodellids, Chromerida and the Apicomplexa - appear to be sister clades. Three other groups - the Perkinsids, Syndiniales and Oxyrrhis are distantly related to the dinoflagellates.
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