This study describes and examines the structural and morphological properties of the hierarchically organized, aragonite cuttlebone forms for the common cuttlefish (Sepia officinalis, L.), including its main structural parts, the dorsal shield, and the chambers. Specifically, it complements the mechanism for the self-organized formation of aragonite, identifies the presence, and determines the role of soluble organic matrix (SOM) proteins in the morphogenesis of the cuttlebone's biomineral structures on the nanoscale. The structure and morphology of the cuttlebone were examined using X-ray diffraction (XRD) and field-emission scanning electron microscopy (FESEM), and their thermal properties by thermo-gravimetric analysis (TGA) and differential thermal analysis (DTA). Proteins from the SOM were investigated using two-dimensional sodium dodecyl sulfate polyacrylamide gel electrophoresis (2D-PAGE), matrix-assisted laser desorption/ionization mass spectrometry (MALDI-TOF MS), nano liquid chromatography tandem mass spectrometry (nano-LC ESI-MS) and Edman degradation. The results showed that the cuttlebone exhibited several diverse biomineral structures characterized by complex morphologies. Their formation is governed by the organic matrix, particularly proteins, which at the earliest stage of development provide templates for the initial extracellular nucleation of the aragonite nanocrystals. This is followed by a bottom-up morphogenesis, based on the nanoscale oriented aggregation and coalescence of primarily formed aragonite nanograins, which results in the hierarchically organized, nanostructured, aragonite forms. The molecular masses of the most pronounced SOM proteins from the dorsal shield were about 10, 15, 40 and 60kDa, while from the chambers they were 10, 20, 25, 30 and 45kDa. Peptide fragments corresponding to Sep7, Sep8, chitin synthase 1, ficoline-2, polyubiquitin and the ubiquitin carboxyl-terminal hydrolase 32-like protein were detected in the SOM, with these proteins having functional properties related to the biomineralization processes. In general, there are mostly acidic proteins present in alternatively glycosylated forms, which are common attributes of biomineralization-related proteins.