The study included 410 samples of shellfish (164 clams, 86 mussels, and 160 shrimps) collected from Suez Canal area as the following: 156 from Port Said, 164 from Ismailia and 90 from Suez governorates. The harvesting water samples (48) were collected from the three sites. All samples were collected during the warmest season (June, July, and August) through two years. After extraction of muscle tissue and homogenization, enriched samples were identified by plating onto TCBS agar medium. Presumptive V. parahaemolyticus colonies were selected, purified, and further identified by API20 and PCR techniques targeting toxRgene. The pathogenicity of the isolates was examined by detection of Thermostable Direct Haemolysin (TDH) and related Haemolysin (TRH) genes. Results revealed that the overall prevalence of V. parahaemolyticus in shellfish was 38/410 (9.27%), where as in water was 12/48 (25%). Higher contamination rate was detected in shrimp (15%), and the highest prevalence was recorded in Ismailia governorate (12.2%). The detection rate of TDH and TRH genes was 21.05% and 5.26% consequently indicating its health hazards to the consumers. This study concluded that the examined shellfish may have the potential human health risk associated with the presence of pathogenic V. parahaemolyticus. The preventative measures should be considered.