After the definitive ban on tin-based antifouling substances, new organic compounds have recently been introduced in antifouling paint formulations, as either principal or booster biocides. In most cases, previous risk assessment of these biocides has been inadequate so that their possible effects on aquatic ecosystems is a matter of great concern. We studied the effects of two new organic biocides often associated in paint formulations, Sea-Nine 211™ (4,5 dichloro-2- n-octyl-4-isothiazoline-3-one) and chlorothalonil (2,4,5,6-tetrachloroisophthalonitrile), on haemocytes of the compound ascidian Botryllus schlosseri exposed for 60 min to various concentrations (from 0.1 to 10 μM) of the xenobiotics. This species had previously proved to be a good bioindicator of organotin compounds. Both compounds, at concentrations of 1 and 10 μM, altered the morphology of phagocytes, and these changes were closely related to disrupting effects on cytoskeletal components. At the same concentrations, phagocytosis, which requires cytoskeletal modifications for pseudopod formation, was severely hindered. Both compounds were able to induce apoptosis of Botryllus blood cells, probably as a consequence of severe oxidative stress related to the reported decrease of intracellular reduced glutathione (GSH) content. In the case of Sea-Nine 211™, a substantial increase in intracellular Ca 2+ and a negative effect on Ca 2+–ATPase activity may also be involved in the activation of the cell death machinery. Cytochrome- c-oxidase was also significantly inhibited by the two biocides, indicating perturbation of the mitochondrial respiratory chain. Isodynamic mixtures of Sea-Nine 211™ and chlorothalonil were used to evaluate the occurrence of interactions between the two compounds. Results suggest the combined action of partial additivity when cell-spreading and cytochrome- c-oxidase activity were considered, and were indicative of antagonism in the case of the GSH depletion. On the whole, our results indicate that short-term in vitro exposure of haemocytes to high concentrations of Sea-Nine 211™ and chlorothalonil provokes a marked reduction in haemocyte functionality, higher than or comparable to that of TBT. These assays of acute toxicity stress the immunosuppressive potential of these compounds, which, although counterbalanced by their short half-life in the marine environment, can lead to biocoenosis dismantling through rapid bioaccumulation by filter-feeding non-target benthic organisms.