Scanning electron microscopy of Peridiniumspecies reveals features of plate structure not visible with the light microscope, in particular delicate ornamentation patterns on the plates. It can also reveal small plates in the vicinity of the flagellar bases that would not otherwise be observed.

Plate number, arrangement and ornamentation (including the features of cryptic plates in the flagellar groove can be of taxonomic value.

Peridiniumcells, like most dinoflagellates, have a nucleus with permanently-condensed chromosomes that lack histones. Mitochondria have tubular cristae. The cytoskeleton is based on an asymmetrical array of two major microtubular roots arising from two flagellar bases. As in other dinoflagellates, a major membranous organelle, the pusule, is found in the vicinity of the flagellar bases. Plastids have thylakoid membranes in groups of three. Pyrenoids may or may not be present.

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