Genus Siganus encompasses a diverse group of fishes with a broad geographical distribution. Siganus rivulatus and Siganus luridus are the most common species of such group in Egypt. The current study introduced an inclusive framework on the molecular characterization and phylogenetic relationship of Siganus species worldwide. Partial sequence of Cytochrome oxidase 1 gene (COI) and D-loop control region were used to barcode S. rivulatus and S. luridus which have been collected from the Mediterranean Sea and the Red Sea in Egypt. Further, the newly assembled sequences were combined with 56 COI sequences representing another 17 Siganus species and 35 D-loop sequences for eight Siganus species, available at the international databases, to reconstruct the phylogenetic relationship among this group of fishes. The analyses performed in the current study included calculation of GC%, calculation of the genetic distance and reconstruction of the phylogenetic relationship among different Siganus species. Based on COI sequences analysis, the average GC% in the studied Siganus species was 46.6%, the genetic distance among Siganus species ranged between 0.004 to 0.166. Based on the D-loop control region analysis, the average GC% was 30.4%, and the genetic distance ranged between 0.048 to 0.346. The COI-based phylogenetic tree clustered the studied species into two major clades. In the first clade, fusiform species inhabiting schools on the inshore reef flats were included. The second clade included deep-bodied species with brightly colored bodies that live on the reef front and those inhabiting the small schools in mangroves, estuaries. In the second clade, S. argentanus, the only species of family Siganidae is known to have a pelagic pre-juvenile stage, was separated into a non-clade group. Whereas, D-loop-based tree grouped S. argentanus in a separate sub-clade with fusiform species. The proper molecular characterization for S. rivulatus, S. luridus and the updated phylogenetic relationship for worldwide Siganus species, provided in the current study, was considered as a primary key for fisheries and aquaculture management for such species.