Abstract The teleost family Mugilidae is speciose with uniform morpho-anatomical characteristics, which render species identification difficult. The dna barcoding technique has, however, proven to be a precise and reliable approach for species delineation. To date, dna barcoding flags numerous polyphyletic species in Mugilidae that probably correspond to species complexes and that call for further taxonomical investigation. Among these species, the squaretail mullet Ellochelon vaigiensis is an interesting case study because, unlike other mullet species, it is easily identified from its unique phenotype. Recent studies of genetic diversity in this monotypic species have revealed two lineages, located either in the Indo-Pacific (Polynesia and Taiwan waters) or along Australian shores. In this study, a third lineage is described in the North of the Indian Ocean, based on nucleotide polymorphisms of Cytochrome c oxidase 1 and barcodes available in bold and Cytochrome b . Despite genetic divergences that exceed the intraspecific threshold, there was no morpho-anatomical difference among specimens of the north Indian Ocean vs. Indo-Pacific or Australia. These molecular results suggest nominal species of Ellochelon vaigiensis within a cryptic species complex.