The heavy metal pollution in seawater and sediment can damage mangrove ecosystems and accumulate in mudskipper that lives in mangrove forests. The accumulation of heavy metal in mudskipper can affect the structure of its gill tissue, liver, and muscles. This research aims at (1) analyzing the levels of Pb, Cd, and Cu heavy metals in mudskipper, sediment, and seawater and (2) analyzing the damage to the gill, liver, and muscle tissue of mudskipper due to the exposure to heavy metals. The mudskipper samples were collected from the mangrove forests of Poka, Waai, and Rutong from May to June in 2019. The heavy metal analysis was conducted using the AAS method, while the gill, liver and muscle tissue staining was carried out with the HE (Hematoxylin Eosin) staining method with 40x magnification. The data were analyzed using descriptive analysis and correlational analysis. The results of the analysis showed that based on the mangrove locations, the order of Pb and Cu accumulation in mudskipper was Rutong> Poka> Waai; while the order of the Cd accumulation was Rutong> Waai> Poka. The changes in the gill tissue structure due to the exposure to heavy metals were in the form of teleangiectasia, secondary lamellar edema, hyperplasia, epithelial desquamation, clubbing, and primary lamellar edema. The changes in the liver tissue structure due to the exposure to heavy metals involved hemorrhage and fat degeneration. The changes in the muscle tissue structure due to the exposure to heavy metals include changes in muscle fibers, edema, and necrosis. The highest accumulation of Pb and Cd was found in gills and muscles from seawater, while low level of heavy metal Cu was found in the liver.