Clinostomiasis is one of the parasitic diseases infecting freshwater fish caused by digenetic trematodes that belong to family Clinostomatidae. During the course of the present study, it was found that 392 out of 520 examined Nile tilapia Oreochromis niloticus were infected with EMC belonging to family: Clinostomatidae with an overall prevalence in (mean ± SD) was 74.12 ± 5.19. The investigated O. niloticus were found to be simultaneously infected with two morphologically different encysted metacercariae (EMC); small cysts (Type 1) ranged from 1.0-3.0 mm in diameter and large cysts (Type 2) were measured 4.0-8.0 mm. Furthermore, an identification of the main morphological features (size of suckers, body length) in both excysted metacercariae was assessed to assist the morphological differentiation of these EMC; namely, Clinostomum complanatum and C. phalacrocoracis. The prevalence rates of C. complanatum and C. phalacrocoracis infections were 35.94± 2.24 and 60.93± 6.70, respectively. In the present study, the molecular identification was carried out by sequencing their COI mtDNA; BLAST analysis of C. complanatum (MT140101.1) showed 100% and 99.74% nucleotide similarity (MK501949.1; MF741769.1) in China, respectively. On the other hand, C. phalacrocoracis (MT140102.1) revealed 100%  nucleotide identity (KY906238.1) in South Africa and 99.66% (KJ786967.1) in Israel.