Fish and marine invertebrates constitute an important part of the human diet worldwide, and their muscles are the major edible parts. The muscles are a rich source of proteins, which in other terms determines the nutritional value and the quality of seafood products. Though the fish skeletal muscle proteins share many similarities with their mammalian counterparts, there exist great differences in their biological activity and structural stability. While the muscles of shellfish or aquatic invertebrates share many properties and general structural features with their vertebrate counterparts, they have unique characteristics. Therefore, understanding the biochemical and physicochemical properties of their major protein components is needed from the viewpoint of effective utilization of aquatic bioresources. Thus, in this review, we aimed to assemble the basis of such differences and also to understand the benefits of these proteins as the targets for studies on the structure–stability relationship of proteins.