Identification of fish species accurately is required to support efforts for conserving fishery biodiversity assessment and sustainable management. Recently, environmental DNA (eDNA) was suggested for regular monitoring of species for effective management of biodiversity. In Oman, molecular reference library representing fish species from the Omani coastline can support such potential approaches. In this communication, we used a local mtDNA-16SrRNA reference library representing Sparidae fish species from the Omani coastlines to identify two Sparidae eDNA sequences (zotu24 and zotu85, from Muscat and Dhofar, respectively) from Acanthopagrus and Diplodus genera reported by a recent eDNA study from Oman. The two species are found to be Acanthopagrus berda and Diplodus cervinus and their sampling sites matches the locations range of the reference specimens. The results indicate the utility and importance for DNA markers’ reference library representing fish species from the Omani coastline to effectively sustain the marine resources using emerging technologies.