Cells of the photosynthetic protist Mallomonas splendens (Synurophyceae, Ochrophyta) are encased within a highly patterned wall or scale case that consists of silicified scales and bristles. In an effort to understand the mechanisms that unicellular protists utilize to produce elaborate, mineralized structures of great complexity and hierarchical structure, we identified and characterized a 41 kDa protein from purified scales/bristles isolated from M. splendens (SP41 for Scale Protein of 41 kDa). A cDNA encoding this protein was isolated and sequence analysis indicated that it is a novel protein. Polyclonal antibodies were generated against bacterially expressed SP41 and used to localize the protein throughout scale and bristle morphogenesis. Immunoelectron microscopy confirmed the biochemical data that SP41 is a component of mature scales and bristles, the protein localizing to silicified components of the purified extracellular matrix. During scale and bristle biogenesis within the cell, SP41 is deposited into a specialized Silica Deposition Vesicle (SDV) concomitant with silica deposition, a highly regulated event during scale and bristle formation. These results argue for SP41 playing a role in morphogenesis and/or silicification within the SDV during scale and bristle biogenesis.