Protistans are a remarkably diverse group of single-celled organisms, all of which are eukaryotic (possessing a nucleus). The issue of how to classify the many kinds of protistans and how to interpret their origins has caused much controversy, and today remains not fully resolved. Recent studies, however, have supported the division of protists into five 'Kingdoms': Rhizaria, Archeplastida, Excavata, Chromalveolata and Amoebozoa. Rhizaria includes amoeboid plankton with mineralised tests (Radiolaria and Foraminifera) as well as cercozoans. Archeplastida encompasses photosynthetic organisms (i.e. with chloroplasts) formed by ancient cyanobacterial endosymbiosis events, including glaucophytes (rare freshwater algae), red algae ('rhodophytes') and green algae ('chlorophytes', technically including the plants, which are multi-cellular and hence not protists!). Secondary endosymbioses of green algae by other eukaryotes lead to the Excavata, which includes the phyla Jakobida, Euglenozoa, Percolozoa and Metamonada (diplomonads and trichomonads), among which we find important human pathogens such as Leishmania, Giardia and Trichomonas. Chromalveolata is a diverse assemblage of algal protists that is thought to have originated from secondary endosymbioses involving red algae. They include the parasitic Apicomplexa (e.g. malaria, Plasmodium falciparum), phytoplanktonic dinoflagellates, ciliates (or Ciliophora), diverse Heterokonta (also known as Stramenopila, and dominated by diatoms), phytoplanktonic Haptophyta (best known for the calcareous-plated coccoliths) and cryptomonads. Finally, the Amoebozoa includes various forms of amoeboe as well as slime moulds such as plasmodial slime moulds (Protostelida) and cellular slime moulds (Dictyostelida), typified by the famous 'social' microbe Dictyostelium. As may be expected, many of these protistan groups provide examples of convergent evolution, most notable of which involve the dinoflagellates.

Dinoflagellates (phylum Dinophyta) are a large group of planktonic algae characterised by two whip-like beating flagella: a longitudinal flagellum pointing posteriorly that propels the cell forwards and a transverse flagellum that controls the direction of travel. For most of its life cycle the dinoflagellate cell is cased in a protective 'cyst' made of organic material (cellulose), and these cysts have been preserved as microfossils in marine sediments since the first appearance of the group in the Triassic (of note, chemical fossils suggest a substantially earlier appearance). The distribution of dinoflagellate populations is controlled by species-specific adaptation to a limited range of temperature, salinity and depth. Although some species inhabit fresh water, most exist as marine plankton and several species periodically form vast algal blooms that can be brightly coloured, neurotoxic or even luminescent. Regarding convergence, polykridid and warnowiid dinoflagellates possess stinging structures that are reminiscent of cnidarian nematocysts and some dinophytes produce saxitoxin, as in some molluscs (e.g. Saxus) crustaceans, fish and cyanobacteria. Among other examples, the endoparasitic dinoflagellate Haplozoon praxillellae stands out, as its form and mode of life mimic that of tapeworms, and also the predatory warnowiids, with their unusual eyes made of modified chloroplasts. Other protistans such as the green algae Chlamydomonas and Volvox have also evolved light sensitive 'eye-spots', notably reminiscent of those in some bacteria, illustrating that such light sensitivity has evolved independently many times. Endosymbiotic dinoflagellates (or 'zooxanthellae') that live inside marine animals show convergence between symbiont species as well as their host organisms, which range from corals and sea anemones to sea slugs, clams and other protists (e.g. foraminifera, ciliates and radiolaria).

Outside the Dinophyta, the convergence between the ciliate Chromidina elegans and dicyemids (in the Lophotrochozoa) is astonishing; both are highly specialised parasites of cephalopod renal organs and have a simplified worm-like form. Certain water-moulds or oomycetes (in the Heterokonta) are strongly convergent with fungal plant pathogens, and in a final and striking molecular example, the mitochondrial gene Cox2 of apicomplexans and green algae show parallel changes in structure and nuclear export.