The current study was carried out to identify suspected causes of septicemia in naturally infected freshwater fishes collected from different fish farms at different localities in Menofiya and Kafr El-Sheikh Provinces, Egypt. Fishes (n=120) were examined clinically and upon post-mortem. Bacteriological isolation and identification of the bacterial pathogens using traditional and molecular methods were demonstrated. Based on the phenotypic and biochemical characterization using API20E, API 20 NE and VITEK® 2 compact, the isolated bacteria were identified as Aeromonads (A. hydrophila and A. veronii). Molecular characterization was accomplished through polymerase chain reaction (PCR) and confirmed by sequencing and phylogenetic analysis. The high molecular identity and close phylogenetic relationship confirmed that the isolates were genetically homologous to A. hydrophila and A. veronii. Thus, this study proves that motile aeromonads remain important bacterial pathogens from aquaculture point of view in Egypt, which requires regular and permanent examination of cultured fishes to resist mass mortalities which lead to economic losses.