The present study investigates the genetic diversity of Scarus ghobban, a recently introduced parrotfish in the Mediterranean Sea via the Suez Canal. Two mitochondrial and one nuclear DNA regions were sequenced and phylogenetic relationships investigated, from samples collected from Lebanon and across its natural range. Scarus ghobban clustered in two major clades, Pacific Ocean and Indian Ocean, indicating strong population structure, or cryptic speciation. Expectedly, Mediterranean samples clustered with Indian Ocean-Red Sea individuals. However, unlike other recent Lessepsian invaders, S. ghobban displayed high genetic diversity. These results underscore that genetic diversity is a poor predictor of success of an invasive species.