Sillaginids are one of the important fishes in coastal waters of Persian Gulf, whose larvae of different species are morphologically very similar to each other and identification of them to species level is very difficult. In this study a total of 4195 Sillaginidae larvae were collected from five inlets (Shif, Lashkari, Ramleh, Dubbeh, Farakeh) and one sampling site in the coastal area of Bushehr Province using a Bongo-net. Morphological and genetic methods were used to identity larvae of this family. The larvae were morphologically divided into two groups, depending on 34 or 38 myomers. The larvae with 34 myomeres were identified as Sillago sihama. To identify larvae with 38 myomers, 12 individuals of postflexion larvae were selected and the morphological characteristic such as number of dorsal and anal fins as well as DNA barcoding of COI were used. According to morphological characteristics, the larvae were divided into two species; Sillago arabica and Sillago attenuata. Genetic studies was done by sequencing of 625 base pair of COI gene. Genetic distances calculated using K2P model between these two species was 18% to 19.7% which indicate that DNA barcoding confirms morphological method and it can be used for identifying younger larvae whose fin rays have not been developed and are unidentifiable with morphological methods.