The creation of carbon materials with controlled micro-architecture and 3D morphology from sustainable and biodegradable natural sources, especially at large scales, is a significant trend in modern materials science. Spongin, a renewable, fibrous biomaterial originating from industrially cultivated marine sponges, is already confirmed as a successful candidate for carbonization up to 1200 °C. This study shows for the first time that centimeter-sized 3D micro-fibrous spongin scaffolds can be carbonized at temperatures up to 2200 °C without loss of structural integrity or sponge-like form. Other biomaterials, even those initially having a 3D structural organization, crumble into powder when carbonized at such temperatures. The results of analytical studies obtained using XPS, Raman, NEXAFS, XRD, ¹³C solid state NMR spectroscopy and HRTEM clearly confirm the formation of turbostratic layered graphite with a surface containing diverse carbon nanophases including graphene, C60 nanocrystallites, and unique rhombohedral graphite with monoclinic C2/m space group symmetry. Examples of potential applications of the prepared graphite constructs are described, along with a discussion of the possibility of high-temperature production of exceptionally stable 3D carbon materials based on spongin.