The levels of mercury in tissues of Penaeus merguiensis from Musa estuary, northwest of the Persian Gulf, were investigated. This study assessed the relationship between mercury levels in hepatopancrea, gill, and muscle with sex, size, and season. The order of mercury concentrations in tissues of the shrimp P. merguiensis was as follows: hepatopancreas > gill > muscle. There was a positive correlation between mercury concentrations in shrimp species with sex and size of its food items. We expected to see higher mercury levels in tissues of female species because they are larger and can eat larger food items. Also, there was a positive correlation between mercury concentrations in shrimp species with its food source. Therefore, female species feed more on shrimp and plant and are contaminated with high levels of mercury. There was significant difference (p < 0.05) in mercury levels between different seasons; higher mercury levels were found in July (summer season).