Abstract Mangrove plants are the most segregated plants, available only in coastal regions around the globe.  A. marina is an important mangrove species and has a wide geographical and climatic distribution, which suggests the presence of large amounts of genetic diversity. A. marina plant samples from four different locations in the Red Sea area were collected. These samples were screened against 8 ISSR markers reported for molecular characterization of mangrove plants. These markers were found to be polymorphic in nature, thus showed 100% polymorphism. On the other hand, enzymatic and non-enzymatic antioxidants are important in plant defense against heavy metals. The present study reported the presence of 9 heavy metals in sediments and mangrove plant parts in the four different locations along Egyptian Red Sea Coast. The levels of four antioxidant enzymes in mangrove plants in these locations were detected. Results showed that the following higher and lower mean concentrations of heavy metals in sediments for the four studied areas by ppm: Cr (7.645±0.37- 40.202±0.09) > Se (9.319± 0.14- 30.522± 0.25) > Zn (1.656±0.09- 5.144±0.03) > Ni (0.01±0.00- 3.161± 0.14) > Au (0.189±0.07- 2.43±0.08 ) > Cu (0.879±0.03 -1.615±0.20) > Pb (0.29 ± 0.04-1.678±0.04) > Cd (0.161±0.04- 0.373±0.03) > Al (0.018±0.01- 0.228±0.07).