In this study, we investigated the mechanism of the indentation size effect based on measurement of the geometrically necessary (GN) dislocation density. The GN dislocation density was measured around impressions by electron backscatter diffraction (EBSD). Indentation tests were performed for two types of single crystal Ni with different crystal orientations: (001) and (111). Difference between (111) and (001) orientation are small in the relationship of the hardness and the penetration depth. However, the deformation behavior and distribution of the GN dislocation density are different for the (001) and (111) orientations. For the (111) orientation, the GN dislocation density increases with decreasing hardness. However, the GN dislocation density for the (001) orientation increases with increasing hardness. The mechanism of the indentation size effect for the (001) orientation can be attributed to the increase of the GN dislocation density. In addition, we investigated the effect of the indenter shape on the indentation size effect. Indentation tests were performed with different apex angles. The hardness using an indenter with a large apex angle is smaller than that using an indenter with a small apex angle. The GN dislocation density increases with decreasing apex angle. The mechanism of the indentation size effect for the apex angle can be attributed to the increase of the GN dislocation density. We prepared another indenter with a dull tip. The hardness using the dull indenter is larger than that using the sharp indenter. The GN dislocation density distribution changes with the indenter sharpness but the GN dislocation density is similar. For the dull indenter, variation of the GN dislocation density has a smaller effect on the indentation size effect than the increase of the resistance because of the different indenter shape.