This study analyzed whether the ownership divergence (the difference between cash flow rights and voting rights of owner managers) can make effects on R&D investments of the firm. If R&D project is successful, corporate value will get higher and shareholders can get profits. However, since the success of a R&D is not certain, managers may not want to take an unnecessary risk. In owner manager companies, agency problems can occur between owner managers and external minority shareholders. Especially when there is big difference between cash flow rights and voting rights of owner managers, the owner manager’s moral hazard can be intensified. The effects of ownership divergence on R&D investment were analyzed and the relationship between them was connected to the level of cash flow rights. Additionally, it was attempted to identify from which shares the negative effects of ownership divergence on R&D investment were made. The empirical evidences are as follows. The ownership divergence made negative effects on R&D investment in the private companies with low cash flow rights of owner managers, which supported hypothesis. In other words, the effects of ownership divergence on R&D investment were confirmed when the size of cash flow rights was controlled. It can be interpreted that low cash flow rights intensify the moral hazard of owner managers. In the further analysis separating cash flow rights and voting rights, entrenchment effect of the voting rights was confirmed and negative effects of ownership divergence were supported.