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Bacterial diseases affecting marine shrimp are numerous and cause high economic losses in marine culture sector in Egypt, therefore; this study was conducted for isolation and identification of some bacteria affecting marine shrimp and have emerged as a significant human pathogen related to seafood consumption in Egypt. A total number of 130 marine shrimp samples were collected from different ordinary market in Alexandria governorate during the period from May 2014 till September 2015 and subjected to bacteriological examination. The bacterial isolates were identified morphologically, biochemically by conventional methods and VITEK 2 system, and Matrix assisted laser desorption ionization-time of flight mass spectrometry MALDI-TOF (MS). The results revealed that the bacterial isolates were mainly isolated from hepatopancrease (49.3 %) followed by Gastro intestinal tract (32.87%) and then abdominal muscles (17.8 %). Vibrio species (V. alginolyticus and V. harveyi) could be isolated mainly during summer (33 isolates) (76.74%) followed by spring (23 isolates) (58.97%) then autumn (11isolates) (45.83%) and it was not recorded in winter. Shewanella algae showed higher incidence during winter (4 isolates) (16.7%) and summer (7 isolates) (16.3%) followed by spring (4 isolates) (10.26%) and it was not recorded in autumn. Also, S. putrefaciens showed higher incidence during winter (6 isolates) (25%) then in summer (3 isolates) (6.97%) but it was not recorded in autumn and spring. The most prevalent bacterium (V. alginolyticus) was identified by PCR targeting dnaJ (species-specific gene) and ToxR (virulence gene) which revealed that out of the 14 tested isolates (14 isolates) (100%) give positive bands for dnaJ gene and (10 isolates) (71.4%) gave positive bands for ToxR gene. [ABSTRACT FROM AUTHOR]