This article is to obtain a picture of the institutional capacity of MRP as a representative institution natives of Papua, the authors use this type of qualitative research methods of interviews and documentation studies. Furthermore, to obtain the validity / validity of the data, then the analysis also uses a qualitative approach. This study was conducted to answer the question, How Institutional Capacity of the Papuan People's Assembly? To answer these questions, theoretical framework is built include: MRP as a means of representation of indigenous people of Papua, institution, authority, recruitment, ethnicity, marginalization and MRP constraints in implementing the tasks and functions. The results of this study indicate, institutions Papuan People's Assembly in carrying out the mandated duties and authorities there are some obstacles or barriers that are often encountered include: The existence of half-hearted political attitude of the government, There is suspicion of government (shadow separatism), The recruitment process specific elements of customary nature of the selection of lower levels, so laden with political dynamics and the politics of money, Even the observer Papua issue, a very strong political intervention from the government, and The establishment of the MRP of West Papua