The issue of representation in the bureaucracy in Jayapura has always been related to the Muslim marginalization in the local government level. In the New Era, government officials were occupied by a combination of Muslims and Christians in a more or less equal. But, after the enactment of Papua special autonomy regulation, many Muslims were fired and only few of them remained in the bureaucracy. The focus of this research therefore lies on why the misrepresentation of Muslims in the government bureaucracy in Jayapura City happens after Papua Special Autonomy? The main issue will be answered through three questions: (1) What is the form of Muslim involvement in the bureaucracy of the Jayapura government? (2) How is the recruitment process of bureaucratic officials in Jayapura government? (3) Is religion a determinant in the recruitment process of officials in Jayapura? This research was mainly conducted in Jayapura City. The data collection is done by observation, interview, and document studies. Observation is focused not only on bureaucratic practices, but also on activities within the Jayapura city government. Interviews conducted beside to Muslim officials, also to religious leaders, adat leaders, and academics to obtain information on the representation of Muslims in the bureaucracy of Jayapura. Document study is done by analyzing the government documents that were related to condition of employee and related matters. This study reveals several interesting findings: (1) the involvement of Muslims in the administrative bureaucracy of Jayapura City is still minimal which is characterized by few officials from Muslim circles, (2) official recruitment is based more likely on primordial ties, especially ethnics and religions. This can be seen from the composition of existing officials, (3) in addition to ethnic issues, religion also gives influence to the determination of officials in the bureaucracy of Jayapura City. This study also found that non-Muslims are the majority in the bureaucracy although it is predominantly Muslim majority area.