Clinostomum (a digenetic trematode) infests tilapia and causes several disease problems. Moreover, Clinostomum has zoonotic importance. Pseudomonas putida is regarded as one of the significant pathogens that have threatened freshwater fishes resulting in high mortality and severe economic loss.  This study investigates the phenotypic and genotypic characterization of P. putida recovered from both fish and their Clinostomum that may bond the Clinostomum infestation to the transmission of P. putida in Tilapia fishes. Fifty P. putida isolates from freshly dead moribund fishes and their Clinostomum, from the Nile River at Al Bahr Al Aazam, Giza, were studied. Also, 5 isolates were retrieved from the water. Biochemical, antibiogram, species-specific PCR and phylogenetic analysis of 16S rRNA gene were performed. Also, Water physicochemical analysis was done. The analysis of water showed bad water quality in summer. P. putida isolates from fish, Clinostomum and water showed the exact antimicrobial susceptibility profile. The phylogenetic analysis of partial 16S rRNA gene sequence revealed that P. putida isolates from fish, Clinostomum and water showed 100% similarity with each other. This result, combined with our isolation of viable P. putida from Clinostomum, proposes the transmission of this serious pathogen through the parasite. In conclusion, the high Clinostomum infestation could play a significant role in the transmission and high prevalence of P. putida in Tilapia fishes in the Nile River at Al-Bahr Al-Azam, Giza.