A system using a microwave induced plasma, as an emission source was optimized for total mercury determinations. The system contains a flow injection section in which mercury is reduced and deposited on a gold:platinum collector, and carried to the emission source. The microwave was generated in a Surfatron cavity. An experimental design was applied to optimize parameters concerning plasma conditions, amalgamation, desorption and mercury vapor generation. The limit of detection of the method was 14 pg ml 1 of mercury, using peak area mode while LDs was 1.3 pg ml 1 using peak height mode, with a 2% RSD and a linear dynamic range of almost three orders of magnitude. The accuracy was assessed using a certified reference material of atmospheric particulate National Institute of Standards and Technology (NIST) 2704. No significant difference at 95% confidence level was observed between the certified value and our results.