Standard microalgae toxicity tests should be able to establish responses in real ecosystems. Natural marine picoplankton samples collected during the months of March, June, August, October 2007 and January 2008, where exposed to 72 h copper toxicity tests. Results analysed by flow cytometry distinguished two groups, with different cytometric characteristics that can match with two of Synechococcus populations. EC(50) values for these two populations resulted low, ranging from 0.62 to 26.28 microg L(-1), this converts copper in a very powerful contaminant and Synechococcus in one of the most sensitive groups of phytoplankton. Differences in EC(50) values for a same population can be related to the month of collection including different initial cellular densities and oceanographic parameters that can affect the picoplankton's tolerance and distribution.