Shell microstructures of five solemyid species from Japan were characterized by scanning electron microscopy. All five species examined had outer and inner shell layers, and were categorized into four groups according to the shell microstructure composition. Group 1 consist of Solemya (Petrasma) pervernicosa and Solemya (Solemya) tagiri. The outer layer of their shells is characterized by radially elongate simple prismatic structure (RESP) type A, and the inner layer by irregular prismatic structure. Group 2 is represented by Solemya (Solemya) pusilla. The outer layer of its shell has RESP type B structure, and the inner layer structure is homogeneous. Acharax japonica is in Group 3. Its outer shell layer has RESP type C, and the inner layer is characterized by laminar, homogeneous, and irregular complex crossed lamellar structures. Group 4 is represented by Acharax johnsoni. Its outer shell layer has a reticulate structure and the inner layer has a cone complex crossed lamellar structure. Reticulate microstructures have never before been found in shells of any molluscan species. These groupings indicate that these solemyid species have a variety of shell microstructures, but the groups are not consistent with previous solemyid systematics at the generic and subgeneric level. Solemyid shell microstructures may provide crucial signals for their phylogenetic grouping, but their significance is not clear from analyses of morphological characters only. In future studies, the utility of microstructural characteristics should be confirmed by mapping the character states of a larger taxonomic sample onto molecular phylogenetic trees.