Microalgae have differing sensitivities to copper toxicity. Some species within the genus Pseudo-nitzschia produce domoic acid (DA), a phycotoxin that has been hypothesised to chelate Cu and ameliorate Cu toxicity to the cells. To better characterise the effect of Cu on Pseudo-nitzschia, a toxic strain of P. multiseries and a non-toxic strain of P. delicatissima were exposed to Cu(II) for 96 h (50 μg l(-1) for P. delicatissima and 50, 100 and 150 μg l(-1) for P. multiseries). Physiological measurements were performed daily on Pseudo-nitzschia cells using fluorescent probes and flow cytometry to determine the cell density, lipid concentration, chlorophyll autofluorescence, esterase activity, percentage of dead algal cells, and number of living and dead bacteria. Photosynthetic efficiency and O(2) consumption and production of cells were also measured using pulse amplitude modulated fluorometry and SDR Oxygen Sensor dish. The DA content was measured using ELISA kits. After 48 h of Cu exposure, P. delicatissima mortality increased dramatically whereas P. multiseries survival was unchanged (in comparison to control cells). Cellular esterase activity, chlorophyll autofluorescence, and lipid content significantly increased upon Cu exposure in comparison to control cells (24h for P. delicatissima, up to 96 h for P. multiseries). Bacterial concentrations in P. multiseries decreased significantly when exposed to Cu, whereas bacterial concentrations were similar between control and exposed populations of P. delicatissima. DA concentrations in P. multiseries were not modified by Cu exposure. Addition of DA to non-toxic P. delicatissima did not enhance cells survival; hence, extracellular DA does not protect Pseudo-nitzschia spp. against copper toxicity. Results suggested that cells of P. delicatissima are much more sensitive to Cu than P. multiseries. This difference is probably not related to the ability of P. multiseries to produce DA but could be explained by species differences in copper sensitivity, or a difference of bacterial community between the algal species.