Marine mussels efficiently adhere under wet conditions by precisely controlling the hierarchical structure of the adhesive plaque through sequential mussel foot protein secretion in the foot-tip cavity. Chemical analysis of the non-uniform mussel plaque morphology has been performed using spectromicroscopy; however, the mesoscopic morphology has not been elucidated yet because of the limited spatial resolution of conventional chemical imaging techniques. We investigated the chemical speciation in the non-uniform mussel plaque morphology employing scanning transmission soft X-ray spectromicroscopy (STXM). The high-spatial-resolution STXM chemical imaging with C 1s near-edge X-ray absorption fine structure yields the distribution of the hydroxy-substituted aromatic residues in the sub-micron scale non-uniform mussel plaque morphology. The matrix consists of a high-protein-density cured product containing a large number of hydroxy-substituted aromatic carbons, including tyrosine and 3,4-dihydroxyphenylalanine (Dopa), whereas the microdomains are poor-protein-density regions with a low aromatic residue relative content. The adhesive interface was covered with the matrix phase to ensure adhesion. The cuticle layer involves a moderate Dopa content, which appears to be optimized for the mechanical performance of the skin.