Mammalian collagens have been used as a base material for collagen matrices in tissue engineering applications. However, collagens of aquatic animals and human sources can potentially be utilized as a safe and viable substitute, because collagen products of bovine origin have been shown to be contaminated with some diseases. In the present study, we prepared and investigated collagen materials from several sources (bovine skin, porcine skin, amniotic membrane and starfish) as matrix biomaterials. Detailed investigations on their physicochemical and biological properties, such as amino acid composition, thermal transition temperature, molar mass, IR spectra, and cell response, suggested strong relations between their amino acid composition and intermolecular structure, thermal property, and cell response. Selectively, an amniotic membrane collagen scaffold was evaluated for cartilage tissue engineering in three types of three-dimensional 3D culture (sponge, gel and micro bead forms) and compared with a bovine matrix. Results showed that amniotic membrane collagen has a potential as an alternative source of collagen for use in tissue engineering.