Halophila stipulacea (Forsskal) Ascherson, a tropical seagrass, is thought to be a Lessepsian immigrant that entered the Mediterranean Sea from the Red Sea after the opening of the Suez Canal (1869). Up to date, no genetic studies of H. stipulacea from Turkey are available. In order to verify the molecular identity of Turkish isolates of H. stipulacea, a part of the rDNA ITS region was sequenced. Comparisons of the genetic polymorphism of this region between isolates from the Turkish coasts of the Aegean Sea and individuals from putative native (Red Sea) and introduced (Mediterranean) populations deposited previously in GenBank were performed. No intra-individual variability was found in the region considered among the isolates from Turkey.