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Abstract This study focused on the validation of the taxonomy, phylogeny and biogeographic distribution of isopods using two marker genes, nuclear 18S rDNA and mitochondrial COI. Isopods were collected from seven host fish species, Liza ramada, Solea aegyptiaca, Tilapia zillii, Pomadasys stridens, Dicentrachus punctatus, Atherinomorous lacunosus and Nemipterus japonicus at four Egyptian lakes, Lake Qarun, Bitter Lakes, Lake Burullus, and Lake Manzala; and two marine localities, Red Sea and Suez Gulf, respectively. The highest prevalence was in Tilapia zillii from Lake Qarun, representing 60% of total collected fishes, while the lowest prevalence was recorded in Solea aegyptiaca from Lake Qarun (8%). The haplotypes recovered from lake isopods belonged to Livoneca redmanii, suggesting the biogeographic expansion of this species among Egyptian distant lake fisheries. A new genus, belonging to the family Cymothoidae, was recorded in the Red Sea fish A. lacunosus. Elthusa vulgaris was recorded in the Suez Gulf fish N. japonicus. The present study aimed to develop new strategic plans for the control of isopods using two model fish (T. zillii and Dicentrachus labrax). The results revealed that D. labrax can combat and eat isopod parasites in their territory. Unexpectedly, there was a clear association between isopod infestations and salinity levels, with the lowest infestation rates occurring in areas with lower salinity. |