The Anzali Wetland is one of the most important ecosystems in the north of Iran, and parts of it were registered as a Ramsar site in 1975. However, even though, due to many problems, including eutrophication produced by inflow of excess nutrients and organic materials, the wetland was also listed on the Montreux Record indicating the need to take urgent remedial action. This study was conducted to study the levels of polychlorinated biphenyls (PCBs) and total mercury (THg) in two fish species (Esox lucius and Carassius auratus) as bio-indicators of the ecosystem condition in eastern part of Anzali Wetland. The sampling was carried out in six different periods between years 2009 and 2010. The results showed that the amounts of PCBs in the muscle of northern pike were below the detection limit of gas chromatography, whereas the average concentration in goldfish was 0.449 mg/kg wet weight. Some possible reasons for the higher levels of PCBs in goldfish in comparison with pike have been discussed. No significant (p < 0.05) correlation was observed between PCBs and biological factors (weight, length, lipid content) for both species. On the other hand, the mean concentration of THg in the muscle of pike and goldfish were 182.22 and 75.27 ng/g dry weight, respectively. Although these concentrations were below US-EPA criterion for human consumption (0.3 mg/kg), it pointed up a significant deterioration of the ecosystem condition during the past years. Finally, statistical analysis revealed a significant correlation between THg with weight and an insignificant correlation with length for pike specimens.