The Pacific oyster Crassostrea gigas is a mollusc with calcium carbonate shell, while the brachiopod Lingula anatina is with calcium phosphate biominerals. Here, we compared ultrastructure observations of the marginal region and the central region of mantles between C. gigas and L. anatina using histology and transmission electron microscopy (TEM) approaches. Our results found both species have similar cell types including the columnar epidermis cell, electron-dense granules cell and electron-transparent granules cell. However, the ultrastructure of the columnar epidermal subtype cells and the inclusion contents of secretory cells in those two species were different. The columnar epidermal cells of C. gigas consists of subtype A that mainly concentrated on the marginal region of mantle, subtype B mainly concentrated on the central region of mantle and subtype C was not common. The sizes of those cells were 7-15 μm. Meanwhile, columnar epidermal cells of L. anatina consist of subtypes A', B' and C'. Their sizes are 10-15 μm. As for secretory cells, both species had electron-dense granules cell and electron-transparent granules cell. However, L. anatina also contained a special class of secretory cells containing lamellar bodies. Those results can partially explain the difference of shell composition between brachiopods and mollusc, and provide reference for the study of shell formation mechanism and mineralization of brachiopods and mollusc.