Gill parasites cause mass mortalities and significant economic losses in the fish industry. This study aimed to identify gill parasites infesting Scomberomorus commerson fish based on morpho-molecular tools and to evaluate their effects on biochemical indices and oxidative stress markers in fish. Eighty fish samples were collected from the Suez Canal in Ismailia Province, Egypt. Mixed parasitic infestation was recorded in 48.7% of fish, comprising Livoneca redmanii isopods and three monogeneans, Cathucotyle cathuaui, Pricea multae, and Pseudothoracocotyla ovalis. Pricea multae had the highest prevalence (67.5%) and intensity (29-80 parasites/fish). This study provided a new occurence of C. cathuaui and P. ovalis from Egypt. The first mitochondrial cytochrome oxidase subunit 1 (cox1) data were reported from the three monogenean species. The two C. cathuaui cox1 sequences were highly homologous and aggregated in a well-supported node in the phylogenetic trees, confirming the morphological identification. The genetic differences and phylogenetic links between P. multae and P. ovalis did not support the Thoracocotylidae family classification. Infested fish showed atrophy, degeneration, marbling appearance, and paleness of gills with excessive mucus secretion. Lactate dehydrogenase, aspartate aminotransferase, and alkaline phosphatase activities were significantly higher in heavily and moderately infested fish compared to the control group. Alanine aminotransferase levels showed a significant increase in the heavily infested group. Superoxide dismutase and catalaze activities significantly decreased in the heavily infested group. Results suggest that the cox1 gene is a valuable marker for identifying monogeneans, and call for controlling gill parasites.