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The present work utilized partial sequences of cytochrome c oxidase subunit I (COI) to study Red Sea populations of threadfin breams (Nemipteridae), and compare their genetic diversity to that of Mediterranean Sea (<i>Nemipterus randalli</i> only) and Indo-Pacific populations. A Maximum Likelihood tree separated four fish species – <i>N. randalli</i>, <i>N. japonicus</i>, <i>N. bipunctatus</i> and <i>N. zysron</i> – into four clades. Haplotype analyses revealed a strong case of the founder effect for the Lessepsian migrant <i>N. randalli</i>: Three haplotypes represented all sampled geographical ranges in the Mediterranean Sea and only one haplotype was shared with a Red Sea individual, presenting evidence that the colonizing population was founded by a small number of migrants. The Red Sea population of <i>N. japonicus</i> shared haplotypes with Persian Gulf and Indian Ocean populations, but South China Sea populations remained fully isolated. The haplotype networks of <i>N. randalli</i> and <i>N. bipunctatus</i> also revealed haplotype sharing between Red Sea and Indian Ocean populations. For <i>N. zysron</i>, one haplotype was shared between Indonesia and the Persian Gulf. We discuss the impact of continued usage of public database sequences of initially misidentified organisms and provide recommendations for avoiding distribution of sequences with incorrect scientific names.