The genotypic characterization of some bacterial pathogens that were incriminated in disease outbreaks among Haffara seabream “Rhabdosargus haffara" and marbled spine foot “Siganus rivulatus" was investigated in full through the current study. A total of 250 fish samples (125 of each species) were collected along the Red Sea coasts of Hurghada City, Egypt. Fish samples were inspected for clinical signs, post-mortem changes, and bacteriological examination. The investigated fishes displayed septicemic signs and external skin lesions characteristic of streptococcosis and tenacibaculosis. Enterococcus spp., Streptococcus spp., and Flavobacterium spp. were isolated from moribund fishes using selective media. These isolates were phenotypically and genetically identified and characterized. The identities of bacterial isolates were confirmed as Enterococcus fecalis, Streptococcus iniae, Enterobacter cloacae, and Tenacibaculum maritimum based on sequencing the 16S rRNA gene. Enterococcus fecalis was the most common pathogen isolated from S. rivulatus and R. haffara and accounted for 46.8% and 47.8% of the total isolates, respectively. Accordingly, the present study proved that Enterocoocus spp., Streptococcus spp., and T. maritimum are important pathogenic bacteria incriminated in wild fish outbreaks in the Red Sea in Egypt. These findings proved the importance of regular and permanent bacteriological examination of wild fish to overcome fish mortalities, which lead to economic losses. Finally, sequencing and phylogenetic relationship techniques proved their usefulness as an ideal assay to develop a reliable, accurate, and rapid detection method for bacterial pathogens in the aquatic environment.