Some plants grown in aquaponic system are affected by bacterial leaf spot disease, with a bad effect on purchasing value. This research was conducted to evaluate leaf spot disease and the bacterial pathogens causative of the disease in aquaponic systems in Egypt. A leaf spot symptom consentient with bacterial leaf spot disease was noticed on several plants grown in six different aquaponic farms in different locations in Egypt during 2016 and disease incidence (%) was recorded. Viable Count (log10 cfu/g) of pathogenic bacteria in cultivated water tank, infected plants and grow bed (plant pots) in six different aquaponic farms in Egypt was determined. In Al-Manashy farm, cultivated water tank and grow bed didn't included any pathogenic bacteria whereas these bacteria involved in different habitats of other tested farms. Pseudomonas sp. disappeared from grow bed of all tested farms except Al-Wahat and Al-Thawra Al-Khadra farm. The distribution of pathogenic bacteria, Xanthomonas and Pseudomonas, on infected plants was assessed in Al-Thawara Al-Khadra farm. Based on morphological and biochemical characterization and disease symptoms, the bacterial isolates belonged to the genera Xanthomonas and Pseudomonas. Pathogenicity test and host range of these isolates were determined on twelve different plants (six hybrids of lettuce: Buterhead, Oakleaf, Rocket, Red Baby Leaf, Watercress, Pock Choi and calendula, cherry tomato, basil, purple kale, hot pepper and spring onion). All the tested Xanthomonas campestris isolates showed pathogenicity on all tested plants except calendula and spring onion, when leaves were sprayed with 1 × 108 cfu/ml of bacterial suspension. Out of nine isolates, two Pseudomonas isolates, namely Ps1 and ps2, recorded the highest values of disease incidence on some tested plants in Al-Thawara Al-Khadra aquaponic farm. More virulence pathogenic bacteria of Xanthomonas and Pseudomonas were identified using 16S rRNA sequencing giving high identities with Xanthomonas campestris campestris and Pseudomonas cichorii respectively.