Four fish species; two fresh water fish (Oreochromis niloticus L. and Tialpia zillii L.), and two marine fish (Liza ramadaL. and Mugil cephalus L.)were used in this study. These species were collected from Damietta and Port Said Governorate, respectively. The current Amplified Fragment Length Polymorphism (AFLP) analysis was successfully able to determine that phylogenetic and reflected the species type and the habitats type. The Nile tilapia and Green-belly were grouped in the same sub-cluster which belongs to fresh water fish, while Toubar and Bouri were found in the other sub-cluster which belongs to marine fish. In contrast to the Principal Coordinate Analysis (PCoA) that showed the habitat in accordance with the majority of life time in fresh water that Toubar spend more time during its life cycle in the fresh water than the Bouri. Structure analysis showed that the Toubar was more closely to the two fresh water species. The ability of these differences among and within species according to Analysis of Molecular Variance (AMOVA) analysis refered to using samples under study with wide environmental range. Our current study for sequence of intron 5 of growth hormone (GH) gene showed differences between L. ramada, M. cephalus, O. niloticus and T. zillii which were successfully able to determine mutations and Deletion and Insertion nucleotides in intron 5 of GH gene between L. ramada, M. cephalus, O. niloticus nad T. zillii. Polymophic single nucleotide and the numbers of A, C, G and T nucleotides for each fragment of intron 5 of GH gene also were determined.