Hexabromocyclododecane (HBCDD) is a brominated flame retardant which is a prioritised substance within the Programme of Existing Substances in the EU. A recent extensive study in Sweden reported traces of the substance in all analysed media both in the environment and in biota. There are no studies, prior to this, on the effect of the compound on brackish water ecosystems. In this study, the ecotoxicity of the compound was investigated in brackish water microcosms (10 l) with natural plankton communities. The communities emerged from sediment and water collected in Öresund. 7 days after the composition of the test-systems they were exposed to the nominal concentrations 50, 100 and 400 μg/l of HBCDD. The zooplankton community was dominated by calanoid copepods and pelagic and semi-benthic rotifers. The direct toxicity of HBCDD resulted in a significant decrease in the abundance of crustacean zooplankton in all tested concentrations, whereas the rotifers were unaffected by the exposure. The total phytoplankton abundance (here including ciliates) increased for all concentrations of HBCDD, probably due to decreased grazing by zooplankton. In total, 7 species of phytoplankton were affected. We conclude from this study that HBCDD has the potential to induce profound changes in thecomposition of natural plankton communities at low (ppb) concentrations.