The emperor fishes, Lethrinus Cuvier, 1829, are generally considered to be ecologically and economically important fishes, occurring primarily in coral reef areas of the Indo-Pacific including the Persian Gulf and Gulf of Oman. The systematics and taxonomy of this genus are complicated due to subtle morphological differences among species. In addition, few molecular studies have investigated the genetic variability of Lethrinus species due to the limited number of taxa and restricted geographic distribution. To achieve this, we constructed a robust phylogenetic tree, various molecular species delimitations and phylogeographic analyses using mitochondrial COI sequences to determine phylogenetic relationships and reveal hidden species diversity in the Persian Gulf and Gulf of Oman. Our phylogenetic results revealed five major clades within Lethrinus with moderate to strong support at nodes. Our findings indicate the existence of at least four unconfirmed candidate species that are well supported by the haplotype network and multiple molecular species delimitations, a finding that contradicts previous taxonomic classification. These results suggest that Lethrinus crocineus, with two genetically distinct lineages, and L. nebulosus, with at least three evolutionarily distinct lineages, represent a cryptic species complex deserving recognition at the species level. In addition, L. lentjan was discovered as a third cryptic species with a robust genetic structure. Five distinct phylogenetic lineages in these complexes were observed in the ecoregions of the Persian Gulf and Gulf of Oman, which have been proven to be hotspots of endemic biodiversity.

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