Naturally occurring nanoorganized biomaterials of marine origin provide an abundant source of novel bone and cartilage replacement materials, and enable the development of novel biomimetic composites. The design of novel biomaterial relies on an understanding of the organic matrices and templating structures. The aim of the present study was to investigate the composition and the properties of skeletal structures of marine sponge (Verongula gigantea) and octocorals (Isidella sp.) in particular by using instrumental analytical (i.e. electron transmission and scanning microscopic methods, vibrational spectroscopies) methods. Modern gentle demineralization techniques were used. It was shown, that the demosponge V. gigantea has much potential as a biomaterial due to the multilayered structure of its rigid fibrous skeletons. The results of FTIR and Raman spectroscopy unambiguously showed that all specimens of the investigated sponge have α-chitin as the main skeletal component. Nano-crystalline aragonite was isolated and identified in V. gigantea, a sponge usually described as lacking a mineral skeleton. Bamboo corals of the Isididae family were additionally investigated. An inorganic component within the deep-sea octocoral Isidella sp. could be clearly identified as calcite by using Raman spectroscopy. The organic part was identified as a nanoorganized fibrillar proteinaceous matrix with acidic properties.