Mitochondria is a cellular source of energy, playing an essential role in cellular stress induced by environmental stimuli. The genetic diversity of mitochondrial genes involved in oxidative phosphorylation affects the production of cellular energy and regional adaptation to various ecological (climatic) pressures influencing amino acid sequences (variants of protein). However, a little is known about the combined effect of protein changes on cell-level metabolic alterations in simultaneous exposure to various environmental conditions, including mitochondrial dysfunction and oxidative stress induction. Present study was designed to address this issue by analyzing the mitochondrial proteins in Fasciola species including Cytochrome C oxidase (COX1, COX2, COX3 and CYTB) and NADH dehydrogenase (ND1, ND2, ND3, ND4, ND5 and ND6). Mitochondrial proteins were used for a detailed computational investigation using available standard bioinformatics tools to explore structural and functional relationships. Our analysis shows that the mitochondrial protein family of Fasciola species are extensively diversified in all species studied, showing an extending role in various biological processes The results showed that the protein of COX1 of F. hepatica, F. gigantica and F. jacksoni consist of 510, 513 and 517 amino acids respectively. The alignment of proteins showed that these proteins are conserved in the same regions at ten positions in COX and CYTB proteins while at twelve locations in NADH. Three dimensional structure of COX, CYTB and NADH proteins were compared and the differences in additional conserved and binding sites in COX and CYTB proteins as compared to NADH were found in three Fasciola species. These results, based on the amino acid diversity pattern, were used to identify sites in the enzyme and the variations in mitochondrial proteins among Fasciola species. This study provides valuable information for future experimental studies including identification of therapeutics, diagnostics and immunoprophylactic interests with novel mitochondrial proteins.