This paper investigates two major frameworks proposed by the media and political and religious leaders to interpret recent Muslim-Christian clashes in Maluku. One de-emphasizes religious aspects in the clashes and explains these in non-religious terms, while the other stresses religious elements and condemns Christians for their maltreatment of fellow Indonesians. After these two frameworks are examined in the second and third section respectively, the fourth section will look at Islamic development for the last few decades in order to place the religious war theory into socio-religious perspective. With this, I will argue that the recent surge of the religious war theory in public discourses is in line with and is an expression of changes in Indonesian Muslim community. Seen from this perspective, peace and harmony among followers of different religions in Indonesia cannot be achieved by the solidification of democracy or by economic stability, but by continuing efforts to promote mutual understanding and to decrease religious hatred.