The most notable shared characteristic is the presence of cortical alveoli, flattened [[vesicle (biology)|vesicle]]s packed into a continuous layer supporting the [[cell membrane|membrane]], typically forming a flexible pellicle. In dinoflagellates they often form armor plates. Alveolates have [[mitochondrion|mitochondria]] with tubular cristae and their flagella or cilia have a distinct structure.
The ancestors of this group appear to have been photosynthetic.<ref name=Reyes-Prieto2008>Reyes-Prieto A, Moustafa A, Bhattacharya D. (2008) Multiple genes of apparent algal origin suggest ciliates may once have been photosynthetic. 18 (13):956-962</ref>
All sequenced mitochondrial genomes of ciliates and apicomplexia are linear.<ref name=Barth2011>Barth D, Berendonk TU (2011) The mitochondrial genome sequence of the ciliate ''Paramecium caudatum'' reveals a shift in nucleotide composition and codon usage within the genus ''Paramecium''. BMC Genomics. 12:272</ref>