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Cheilinus trilobatus, Cheilinus quinquecinctus, and Chlorurus sordidus specimens from Saudi Arabia's Farasan Islands were collected and genotyped using inter simple sequence repeats (ISSRs) and start codon targeted (SCoT) primers. Mitochondrial cytochrome C oxidase subunit I (COI) gene fragments were used for DNA barcoding. ISSRs and SCoT primers showed moderate polymorphisms: expected heterozygosity (Hexp) of 0.470 and 0.435 and average polymorphism information contents (PICs) of 0.359 and 0.339 for ISSRs and SCoT markers were observed, respectively. Cheilinus quinquecinctus had the highest genetic diversity from ISSRs (70%) and SCoT (73%). Chlorurus sordidus and C. trilobatus showed similar genetic diversities of 29% and 39% based on ISSRs, respectively, and 60.32% for both species based on SCoT. Cheilinus quinquecinctus had the lowest nucleotide diversity (π) of 0.003, while C. sordidus and C. trilobatus had π values of 0.065 and 0.103, respectively. Analysis of molecular variance (AMOVA) revealed greater genetic variation among species rather than within them using ISSRs (65% and 67%, respectively) and SCoT (35% and 33%, respectively). COIbased AMOVA showed similar genetic variation among (51.11%) and within (48.89%) species. The current study highlighted outperformance of COI compared to ISSRs and SCoT markers in differentiating among parrotfish species. Also, ISSR outperformed SCoT since it was able to clearly show three distinct groups in principal component analysis. This study also confirmed the presence of three distinct parrotfish species, which will provide an insight into parrotfish diversity. Moreover, the results will contribute to monitoring parrotfish migration between Farasan Islands and different geographic locations which significantly affect species conservation. [ABSTRACT FROM AUTHOR]