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Dinoflagellates have been regarded as bizarre products of evolution. They belong to one of the most strongly supported macrolineages among the protists, the superphylum/kingdom Alveolata, which contains three main phyla: the Dinoflagellata, the Apicomplexa and the Ciliata. These organisms all have cortical alveoli and micropores. Until the early 1990s, living and fossil dinoflagellates were classified separately and both relied almost exclusively on morphological characters. During the early 1990s, fossil and living taxa were brought together in a detailed morphological classification that emphasized tabulation. Since that time, molecular studies have supported many morphological groups, but have shown others to be paraphyletic. Our understanding of phylogenetic relationships within the dinoflagellates has changed as more taxa have been described and more genes have been analysed. Relationships among the lineages also vary widely with the algorithm used to analyse the data. A highly unusual and notable feature of dinoflagellates is the variety of plastid types that they have acquired by secondary and even tertiary symbiosis; indeed, they possess the most diverse array of plastids of any eukaryotic lineage and they are truly the kings of symbioses. Genome rearrangements have taken place as the plastids evolved. The genes that have moved to the nucleus in dinoflagellates with peridinin plastids are different from those moved in all other eukaryotes; moreover the few genes left behind in the peridinin plastid have become uniquely arranged into mini-circles. Where tertiary endosymbiosis has taken place, the plastid genome was rearranged again. Mitochondrial modifications in the dinoflagellates are also unique among the eukaryotes. While study of these factors remains critical in understanding dinoflagellate phylogeny, the fossil record continues to contribute by presenting morphologies that are unrepresented (or under-represented) among extant taxa; such observations can suggest relationships to be tested by molecular analyses.

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