The four flagella are each coated with three discrete layers of organic (polysaccharide-containing) scales; pentagonal scales, rod scales and hair scales. The theca is also composed of polysaccharide scales; because the individual scales are fused together, the scale-based structure of the theca is not apparent in all preparations. All scales are formed in the Golgi apparatus, which is found in the anterior end of the cell adjacent to the flagellar bases.

The flagellar apparatus consists of four flagellar bases, four microtubular roots, and two massive striated roots (rhizoplasts), located at the base of the apical depression. The arrangement of these elements approaches 180 rotational symmetry (a kind of radial symmetry). The flagellar bases are nearly parallel to each other, and their proximal ends are mounted in nearly a straight line. Complex structures, sometimes called "half-desmosomes", link each of the microtubular roots to the cell membrane a short distance from the root origin. The rhizoplasts, which connect the basal bodies to the nucleus, are contractile, in response to changes in calcium-ion concentration. Centrin is a, perhaps the, major structural protein in rhizoplasts.

Few differences are noted between species in scale and flagellar apparatus features.

The pyrenoid is usually located immediately posterior to the nucleus. The pyrenoid typically is surrounded by starch grains, and is penetrated by cytoplasmic channels which may have lobes of the nucleus within. The structure and content of these channels supply the principal characters used to identify subgenera of Tetraselmis.

Cell division is marked by a "metacentric" spindle. The spindle poles form in the vicinity of the rhizoplasts, which disassemble. Flagella are shed, but the flagellar bases persist and, after replication and migration, lie lateral to the spindle poles. At cytokinesis, microtubules arising from the flagellar base complexes ("phycoplast" microtubules) line the cleavage furrow that eventually separates the cells.

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