Abstract Dinoflagellates are marine organisms that undergo seasonal explosive proliferation events known as algal blooms. Vegetative cell proliferation is a main contributing factor in these events. However, mechanistical understanding of mitosis and cytokinesis in dinoflagellate remains rudimentary. Using an optimized immunofluorescence protocol, we analysed changes in microtubule organization occurring during the mitotic cycle of the toxic dinoflagellate Ostreopsis cf. ovata. This study revealed important features of dinoflagellate cell division. We find that the two flagella and the cortical microtubule array persist throughout the mitotic cycle. Two microtubule bundles are present in the cytoplasm originating from the ventral area, where the basal bodies are located: a cortical bundle and a cytoplasmic ventral bundle. The latter associates with the nucleus in the cell centre in preparation for mitosis and with the acentrosomal extranuclear spindle during mitosis. Analysis of tubulin post-translational modifications identifies two populations of spindle microtubules: polar acetylated microtubules whose length is stable throughout mitosis and central tyrosinated microtubules which elongate during chromosome segregation. During cell division a microtubule rich structure forms along the dorsal-ventral axis, associated with the site of cytokinesis, consistent with a cytokinetic mechanism independent of the actomyosin ring typical of animal and yeast cells. Summary statement Our study describes special features of mitosis and cytokinesis in dinoflagellates and uncovers a new alternative mechanism for cell division, highlighting the plasticity of cell biological process in eukaryotic cells.