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The recent invasion of the lionfish Pterois miles to the Mediterranean draws major concerns to the fate of the indigenous ecosystem, based on previous knowledge of the species' detrimental capabilities as an introduced species in the Western Atlantic Ocean. In order to determine invasive patterns in the Eastern Mediterranean, we compared the genetic divergence of two mtDNA markers, the COI and D-loop, between and within the introduced Levantine and native range Red Sea populations of the lionfish. COI region presented a remarkably shallow genealogy, and both genes have failed to show a definite geographic population structure, with non-significant AMOVA and low pairwise FST values. A shared haplotype across all localities in the D-loop provided probable confirmation for the Red Sea origin of the invasive population, and a number of introduced haplotypes indicated that the Mediterranean populations are a product of multiple invasion events. Finally, we observed large haplotype diversity in the Red Sea samples that were absent from the introduced localities, implying a possible future enforcement to the invasive genetic pool in the Mediterranean Sea.