Although the assumption has long been made that the Ciliophora arose from flagellates, limited progress has been made in determining exactly what extant group - flagellate or other - may best resemble the ancestral "preciliate" assemblage. The distinctiveness of the ciliates and of the many protist phyla containing flagellated stages in their life cycles makes the recognition of potentially homologous features difficult. The suggestion that there may be a phylogenetic relationship between dinoflagellates and ciliates, while seeming unlikely from consideration of a number of specialized characters, is attracting increased attention. This is because some basic similarities (possibly shared derived characters) are characteristic of many species from both groups: cortical alveoli, tubular mitochondrial cristae, kinetidal systems, acentric mitoses with persisting nuclear envelope, functional cytostome, extrusomes (mucocytsts and explosive trichocysts), locomotory organelles, and small subunit rRNAs (close structural similarity values). But many questions remain unanalyzed or unanswered, and caution is still advisable in drawing any firm conclusions about the evolutionary closeness of ciliates and dinoflagellates.