The most complicated live organism relationship is between parasites and their hosts. Since this interaction has increased attention because parasites have been shown to have a major impact on population dynamics and the ecology of their hosts. The existing relationships between hosts and parasites have developed through antagonistic interactions, leading to coevolutionary processes that result in intricate reciprocal adaptations. Through these adaptations, parasites can take advantage of the biological characteristics of their hosts, which helps to ensure their survival, spread, and continued viability as a population. Parasitism has been linked to variations in various aspects of fish behavior, including foraging efficiency, habitat preference, shoaling behavior, predator-prey interactions, competitive prowess, swimming ability, and sexual behavior, as well as mate selection. Fish also use techniques to reduce the risk of contracting parasites, such as avoiding certain habitats, selectively targeting prey, or steering clear of infected individuals. Additionally, they may engage in behaviors aimed at removing parasites, such as scraping against substrates or seeking out cleaning stations. Clinostomum sp. are digenetic trematodes characterized by genetic diversity and intricate life cycles involving three hosts: snails, fish, and birds. The larval stages of these parasites have a deep impact on the freshwater aquatic systems, particularly when infecting the second intermediate host, fish. Unfortunately, there have been no studies conducted on the morpho-molecular characterization of Clinostomum sp. from freshwater fishes in the Sultanate of Oman. Furthermore, the prevalence of Clinostomum sp. on freshwater fish remains unstudied, hindering efforts to comprehend its life cycles, develop control strategies, and evaluate its impact on freshwater fish and aquatic ecosystems in Oman. Therefore, there is environmental and epidemiological research linked to Clinostomum parasites needed in freshwater fish within Oman. In the present study, the Killifish Aphaniops sp. was selected as the principal species due to its prominence in Omani freshwater ecosystems to evaluate the prevalence and intensity of Clinostomum sp., characterize these parasites using a morphomolecular approach, and unveil their pathological effects on the host fish. Live fish specimens were sampled from four distinct locations in the Muscat region: Al Amirat, Al Khoud, and Darsait and Al Bahayes. All fish samples were measured length and weight to compare parasite populations at the four different locations and fish sizes. In addition, the data of parasites was categorized depending on infection locations and genders of host fish. For identification of Clinostomum sp. morphologically characterized metacercaria as measuring various organs of the parasite, identified them through DNA sequences from nuclear 28S-rRNA (28S). Randomly selected 5 fish from each sample site were divided into five sections to accommodate sizing for cassette fixation and to focus on the most heavily infected body part and completed with H&E staining to study the histopathological impact of the parasite on the host fish. In the regions of Al Khoud, Darsat, and Al Amirat, 50 Killifish Aphaniops were gathered, with 39, 42, and 40 fish found to be infected, respectively. Conversely, in Al Bahayes, a total of 23 fish were collected, with no parasitic infection observed across all samples. In other words, the prevalence of Clinostomum sp. was highest in Darsat at 84%, followed by Al Amirat at 80%, Al Khoudh at 78%, and then Al Bahayes at 0%. The parasites were infected more with females than males and the large size of the fish at all sampled locations (P0.05). More Clinostomum was found in the trunk region of the host fish than head and tail regions. Morphological measurement of parasite result showed that Clinostomum on the host fish from Omani freshwater body was clearly outranged (rather smaller) of existed two species of Clinostomum species (Clinostomum complanatum and Clinostomum maginatum). More certainly, the DNA sequence result showed Clinostomum from Oman was very close to Turkish Clinostomum complanatum but not the same species. The histopathological impact of the fish tissue revealed the presence of Clinostomum within the tissue layers. Lesions in the cavity tissues aligned with the destructive inflammatory response and cyst encapsulation from infection. The present study confirmed Clinostomum sp. caused tissue inflammation and the subsequent destruction and perforation of tissues of fish host. The present study contributes valuable information to the understanding of the host-parasite interface within freshwater ecosystem in freshwater ecosystems. The findings emphasize the importance of continuous research and monitoring to develop comprehensive strategies for mitigating environmental hazards and to conserve healthy aquatic ecosystems.