Nuclear features of dinoflagellates that were used originally to support the Mesocaryota concept are reviewed. The fibrillar diameter of dinoflagellage chromatin, low level of chromosomal basic proteins, membrane attachment of chromosomes and swirl pattern observed in sectioned chromosomes are features that support a prokaryotic affinity. The presence of repeated and highly complex DNA, a S-phase of DNA synthesis in the cell cycle, presence of basic proteins, and the reinterpretation of extranuclear microtubules as a spindle support the contention that dinoflagellates are eukaryotes. This combination of prokaryotic and eukaryotic features suggests that dionflagellates are a geologically old group and that perhaps they diverged from the higher eukaryotic lineage before evolution of eukaryotic chromatin but after the evolution of repeated DNA. The 2 patterns of carotenoid composition exemplified by the presence of peridinin or fucoxanthin suggest separate origins of dinoflagellate plastids, perhaps by prokaryotic and eukaryotic capture. It is suggested that the species possessing fucoxanthin obtained their plastids by capture of photosynthetic eukaryotes.