This study investigated the effects of governing structures focused on the relationship between perceived goal discordance and styles of conflict resolution at food service franchises. In particular, this has applied multi level prospective to recognize the influence of conflict rather than one level which is insufficient to decide it in the franchise of headquarter organization. Data were collected by different levels of 32-franchisers and 375-franchisees. The analysis of HLM indicated that at the franchisee level, perceived goal conflicts were significantly related to the franchisee`s styles of conflict resolution (collaborating and avoiding style). At the franchisor level, the relational governance was significantly related to all styles of conflict resolution(collaborating and aggressive style). The contractual governance was significantly related to only aggressive style. Moreover, governance structure at the franchisor levels was proved to be as a moderator on the relationship between conflicts and collaborating and avoiding style. The results contribute the franchise literature by applying a multi level perspective.