The most notable shared characteristic is the presence of cortical alveoli, flattened vesicles packed into a continuous layer supporting the membrane, typically forming a flexible pellicle. In dinoflagellates they often form armor plates. Alveolates have mitochondria with tubular cristae, and their flagella or cilia have a distinct structure.
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 linages, 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.
Relationships between some of these the major groups were suggested during the 1980s, and between all three by Cavalier-Smith, who introduced the formal name Alveolata in 1991. They were confirmed by a genetic study by Gajadhar et al. 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 development of plastids among the alveolates is uncertain. Cavalier-Smith proposed the alveolates developed from a chloroplast-containing ancestor, which also gave rise to the Chromista (the chromalveolate hypothesis). However, as plastids only appear in relatively advanced groups, others argue the alveolates originally lacked them and possibly the dinoflagellates and Apicomplexa acquired them separately.