We studied the effects of pollution in the colonial ascidian Pseudodistoma crucigaster at organismal and suborganismal levels. Our goal was to find early biomarkers to detect some effect of pollution before changes in community structure or species composition occur. We examined the effect of Cu on the production of heat-shock proteins, defence metabolites, growth rates and presence of resistance forms. We performed a transplant experiment to a Cu polluted harbour and observed negative growth and presence of resistance forms but not depressed production of toxic metabolites or an increase in stress proteins (hsp) in the ascidian. In a laboratory experiment, stress proteins were induced only under half the Cu concentration found in the harbour. We conclude that hsp can be used in this ascidian as an early warning system for sublethal pollution but that the response is inhibited above a threshold of the stressing agent, which may vary among species.