Oysters and blue mussels are important hydrobiological resources for aquaculture. In Chile, they are farming on the Chiloé island, where around 18% of the world's mussels are produced, however, their nutritional dynamics are largely unknown. For this reason, the objective of this study was to determine the proximal biochemical composition and the fatty acid profile in the Chilean oyster (Ostrea chilensis), the Pacific oyster (Crassostrea gigas) and the Chilean mussel (Mytilus chilensis), to perform an intra and interspecific comparison. Shellfish sampled in winter were characterized by a high protein content, followed by medium values for lipid content and a low carbohydrate content compared to similar species in Europe. Also, oysters and mussels were found to be rich in omega-3 long chain polyunsaturated fatty acid (n-3 LC-PUFA), so they can be considered excellent functional food option for a healthy human diet. Their high contribution of n-3 LC-PUFA ranged between 5.2-12.9 μg FA mg-1 dry weight with high n-3/n-6 ratios, which depends on both the species and the on-growing location. Both taxa can be considered a plausible option to promote a healthy diet of marine origin in future generations. Also, these results could benefit the projection and development of aquaculture of these mollusks.