Political dynamics of minority group inside a minority community in a separatist movement setting is still understudied. Many studies are portraying minority community struggle vis a vis majority community in hostility situation. Yet, a community is never homogeneous; there are always minor groups with different aspirations or dissimilar backgrounds. My study acknowledges the Muslim Papuan minority's political struggle under the Papua separatist conflict. The Muslim Papuan shares same identity with the majority community in Indonesia and it is different with the majority of Papuan fellows that are Christians. Muslim Papuan also experienced marginalization in the society. However, their political choice is to side with the majority Papuan. The main argument is that the Muslim Papuan community's political preference is the result of identity struggle in their own motherland. Moreover, the paper seeks to assess the possibility of the minority groups as the agent of peace. It is found that the prospect will only occur in the loosened security tension and a situation is most likely not to occur soon in Papua conflict.