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Background: Aquatic ecosystems pollution with heavy metals, especially mercury, has always been a major concern for aquatic organisms health. Hence this study not only described an innovative method for analyzing organic mercury compound, but also evaluated total and organic mercury concentrations in great cormorant and compared them with world health standards. Materials and Methods: In this cross-sectional study, 18 great cormorants were randomly captured in March, 2009. Total and organic mercury of muscle, kidney, and liver tissues were analyzed by an advanced mercury analyzer made in the United States (Model Leco, AMA 254), and statistical analysis was done by Mann-Whitney U, and Kolmogrove-Smirnov tests. Results: Mean accumulated total mercury in liver, kidney, and muscle tissues were 5.67, 3.59, and 2.26 mg kg -1 w.w., respectively and organic mercury formed 82, 79, and 58 % of the total mercury. Conclusion: The levels of accumulated mercury in all tissues of great cormorant were more than the established limits by WHO, FAO, and EPA. These results can be a serious warning for consumers of these birds, especially vulnerable people.