For a long time, chitin was not recognized as an integral part of certain sponge skeletons. The origin of this chitin is not entirely clear since the presence of chitin synthase genes in the genome of the corresponding sponges has not yet been studied in detail. The first observations of chitin-based scaffolds in Verongida sponge skeletons were recently reported by our group in 2007. Today, these three-dimensional nanostructured tube-form scaffolds have been characterized by a broad variety of modern bioanalytical and physicochemical techniques in order to determine their morphology, composition, and structure. These results are represented and critically discussed in this chapter. We succeeded in the discovery of a 505-million-year-old chitin in the basal demosponge Vauxia gracilenta and in the discovery of chitin in freshwater sponges such as Spongilla lacustris and Lubomirskia baikalensis. We have also isolated and characterized six new chitin synthase gene fragments from the freshwater sponges studied. The presence of chitin in both marine and freshwater sponges indicates that this important structural biopolymer was already present in their common ancestor. During the last few years, we succeed in developing a novel method for the production of three-dimensional cleaned chitin skeletons from dictyoceratid sponges and the use thereof for tissue engineering and stem cell research. Furthermore, for the first time, we proposed sponge chitin as a thermostable biological material for the development of next generation of nanostructured biocomposites using “extreme biomimetic conditions” via a hydrothermal synthesis route.