The taxonomy of three Recent Spinileberis species (S. quadriaculeata, S. furuyaensis, S. pulchra) and one new fossil species, S. lubrica sp. nov. from Japan was studied, and the phylogenetic relationship between the four species was also considered. The relationship with S. lubrica sp. nov., which is an extinct species, was analysed by comparing its carapace morphology with those of the three living species. On the basis of the observation of the cross-section of four Spinileberis shells, the crystallographic structure of the valve is similar between S. pulchra and S. furuyaensis, and S. quadriaculeata and S. lubrica sp. nov., respectively. On the other hand, the relative thickness of the valve is variable among the four Spinileberis species. The same number and similar distributional pattern of normal pores between S. lubrica sp. nov. and S. quadriaculeata suggest that S. lubrica sp. nov. evolved from the common ancestor of S. quadriaculeata and S. lubrica sp. nov. A consideration of the characteristics of the new fossil species, together with the three recent ones, leads us to believe that the species of the inner bay of Japan, S. lubrica sp. nov., is likely to have adapted to very fine sand or silt with relatively high-salinity water, in contrast to the other three Spinileberis species. The complete male soft parts of S. furuyaensis are also herein described for the first time.