Genetic diversity across Tilapia species is important key fordevelopment aquaculture strains, protection of endangered populations and biogeographical inferences. Total soluble protein and esterases isozymes were extracted from flesh (muscles) and liver of all individuals from the three populations (Ryad, Bahr El-Baqar and Motobs) from each species under study to estimate the genetic diversity. With comparing the obtained bands from the three Oreochromis niloticus, it was found that 13 bands out of the 20 were common bands among the three populations. The three T. zilli populations exhibited 8 bands out of the 21 were common bands among those three populations. The three O. aurea populations exhibited 10 bands were common between three populations, while the rest of bands appeared in some of population and disappeared in the other. Ryad and Motobs individuals of O. niloticus showed four isozymes. Meanwhile, Bahr El-Baqar exhibited only three. Ryad and Bahr El-Baqar individuals of T. zilli showed three isozymes. Meanwhile, Motobs exhibited four ones. Maximum two isozymes were detected in population of O. aurea. Band 1 was dark in Ryad individuals and ranged from very faint, faint and dark in Bahr El-Baqar and Motobs. The phylogenetic relationship within the studied populations of the three locations concerning O. niloticus, T. zilli and O. aurea was conducted and different variations were detected. Population from Ryad was highly differentiated than other populations.

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