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Classification

Alveolata include around nine major and minor groups. They are diverse in form, and are known to be related by various ultrastructural and genetic similarities:

The Acavomonidia and Colponemidia were previously grouped together as colponemids, a taxon now split because each has a distinctive organization or ultrastructural identity. The Acavomonidia are closer to the dinoflagellate/perkinsid group than the Colponemidia are. As such, the informal term "colponemids", as it stands currently, covers two non-sister groups within Alveolata: the Acavomonidia and the Colponemidia.

The Apicomplexa and dinoflagellates may be more closely related to each other than to the ciliates. Both have plastids, and most share a bundle or cone of microtubules at the top of the cell. In apicomplexans this forms part of a complex used to enter host cells, while in some colorless dinoflagellates it forms a peduncle used to ingest prey. Various other genera are closely related to these two groups, mostly flagellates with a similar apical structure. These include free-living members in Oxyrrhis and Colponema, and parasites in Perkinsus, Parvilucifera, Rastrimonas and the ellobiopsids. In 2001, direct amplification of the rRNA gene in marine picoplankton samples revealed the presence of two novel alveolate lineages, called group I and II. Group I has no cultivated relatives, while group II is related to the dinoflagellate parasite Amoebophrya, which was classified until now in the Syndiniales dinoflagellate order.

Some studies suggested the haplosporids, mostly parasites of marine invertebrates, might belong here, but they lack alveoli and are now placed among the Cercozoa.

The ellobiopsids are of uncertain relation within the alveolates. Silberman et al 2004 establish that the Thalassomyces genus of ellobiopsids are alveolates using phylogenetic analysis, however as of 2016 no more certainty exists on their place.