The present study was planned to investigate the phenotypic and genotypic characterization of bacteria isolated from shrimps in Suez Canal area.
A total number of 210 shell diseased shrimps (Penaeus japonicas) were collected.Isolation of 732 isolates from shrimp muscles, cuticles, gills, haemolymph and hepatopancrease and were identified according to the morphological and biochemical tests to vibrio species (Vibrio alginolyticus and Vibrio parahemolyticus) and others. The number of isolates for Vibrio alginolyticus was 568 isolates by incidence of 77.59%, Vibrio parahemolyticus was 131 isolates by incidence of 17.89%. Clinical signs observed on naturally infected shrimps included dark brown to black patches scattered all over the body surface including the cuticle of the carapace, abdominal segments, uropod, pereopod (walking legs) and pleopod (swimming legs). With necrotic focci most frequently located on the cuticle of the abdominal segments. Necrosis and destruction of the periopods, pleopods and the antennal flagellum.  The eyes of some moribund shrimps were affected and became protruded and edematous (Exophthalmia). Postmortem findings included black colored gills with adhesion of gills lamellae, and there were swelling and congestion of hepatopancreas and heart, also the haemolymph changed their colour to orange (bloody haemolymph). PCR protocol used for amplification and detection of 16S rRNA gene for all Vibrio isolates, and gyrB gene, toxR and ompK virulent genes for V. alginolyticus, and flaE gene, tdh and tlh virulent genes for V. parahaemolyticus isolates to confirm the diagnosis of these isolates, the positive amplification of 16S rRNA gene showed at 663bp fragment of the extracted DNA of all vibrio isolates, the positive amplification of gyrB gene, toxR gene and ompK gene showed at 340bp, 173bp and 319bp fragment respectively of the extracted DNA of V. alginolyticus and the positive amplification of flaE gene, tdh gene and tlh gene showed at 897bp, 269bp and 450bp fragment respectively of the extracted DNA of V. parahaemolyticus.