Since its introduction in the early 1980s, the invasive freshwater crayfish Procambarus clarkii has flourished in the River Nile. Its distribution now spans from the Delta region and Giza in the north to Aswan in the south. The economic importance of this species in Egypt has increased over the past decade, as reflected in the significant rise in the export of processed and live animals to China and the USA. Crayfish processing factories along the River Nile heavily depend on fisheries targeting this species, further enhancing its economic value in Egypt. The present study aimed to assess the genetic variation in the COI gene of P. clarkii from the Giza and Aswan populations in comparison to native USA populations. Isolates collected from Giza were closely related to P. clarkii, with a similarity index of 99.41%, while isolates from Aswan were also closely related, with a similarity index of 99.26%. Aswan isolates are derived from the Giza isolates. Egyptian isolates show the closest relationship to Chinese isolates, both of which are descended from the United States isolates. Furthermore, the nutritional composition of the flesh was evaluated during different fishing seasons to assess its nutritional quality in the two locations. The levels of lipids and proteins were significantly higher in Aswan than in Giza, in both sexes and during the summer season. This suggests that the flesh from the southern regions of Egypt is of a higher quality.