The microstructure observation of seed surface structure is needed for protocols of breaking dormancy of seeds with physical dormancy. The seeds of Rubus species are surrounded by a thick, hard endocarp; together, the seed and endocarp make up the stone. We evaluate stone characteristics of 18 species of Rubus through optical microscopic observation, and correlate different stone characteristics with endocarp thickness. As a result of stone size comparison, Rubus species were classified as big stones group including R. parvifolius and R. idaeus, small stones group including R. longisepalus var. longisepalus, R. corchorifolius and R. hirsutus, and middle stones group including rest of the species. The result of this study revealed that stone size and the endocarp thickness in Rubus species was various characteristics in each species. Furthermore stone size and stone weight were also well correlated endocarp thickness and result indicated that heavy stones had harder endocarp than lighter one. Thus from the result of this study it can be presumed that only one stone characteristic approach may be sufficient to estimate other characteristics in Rubus.