Parathion, an organophosphorus insecticide, is highly toxic to the two free‐living marine dinoflagellatesProrocentrum micansEhrenberg (autotrophic) andCrypthecodinium cohniiBiechler (heterotrophic). To study its non‐antiacetylcholinesterase action we assessed its effect on the mitochondrial system, as shown by changes in intracellular ATP concentration and in rhodamine 123 fluorescence evaluated by image analysis. The technique of image analysis permits direct assessment of changes in the overall activity of mitochondria in living cells. Mitochondrial structures were also examined in the electron microscope. The three methods of investigation yielded complementary results. InP. micans, parathion noticeably altered mitochondria but did not significantly alter ATP concentrations. InC. cohnii, however, mitochondrial disturbance was slight, whereas ATP increased greatly. We think, therefore, that parathion has different effects on mitochondria in the two organisms, and in particular that it increases mitochondrial activity inC. coh