Morphological characteristics and electrophoretic protein patterns were considered in the present study to distinguish between two types of clinostomatid metacercariae from Oreochromis niloticus fish caught from the River Nile at El-Minia district, Egypt. Fifty-two specimens of randomly collected 120 examined fish were infected with both Euclinostomum ardeolae and Clinostomum phalacrocoracis metacercariae or either. Euclinostomum ardeolae metacercariae were embedded in Oreochromis niloticus tissues of the kidney as round to oval greyish black cysts giving the area around faint black color with a 15% prevalence rate of infection. Cyst was of variable size (3-4 mm) and thin completely tight wall. Metacercaria is aspinose pyriform in shaped, long 6.5 wide 2.3 mm, of blunt anterior end but the posterior one is nearly rounded. Clinostomum phalacrocoracis yellow to orange in color cysts were detected in the pharyngeal region and branchial chambers and the prevalence rate of infection was 39.16%. They varied in size (4-5.2 mm) with a thin transparent membrane full of yellowish fluid. The body of metacercaria was elongated, tongue-shaped, and slightly wider in gonadic region, long 16.4 wide 4.01mm. Electrophoretic protein profiles were resolved using one dimensional SDS-PAGE stained with Coomassie Brilliant Blue R-250 stain. Encysted and excysted Euclinostomum ardeolae metacercariae showed bands of 61 kDa, 29 kDa, 28 kDa, 15 kDa and 14 kDa, while Clinostomum phalacrocoracis encysted and excysted metacercariae revealed bands of 61 kDa, 54 kDa, 32 kDa, 31 kDa, 20 kDa, 17 kDa, 15 kDa and 14 kDa. Conclusively, biochemical findings are in concordance with morphological characterization confirming both metacercariae to be of two distant species.