This research was driven by the fact that Shia presence and its involvement in sectarianism conflict in Indonesia had received little research attention. The research examines the ways in which this conflict is conceptualized within court decisions. The aim of this paper is to analyze the motives and the impact of the sectarian conflict in Madura 2011-2012, which was caused by allegations of religious wrongdoings. Although it can be interpreted that individual and group beliefs, along with their religious denominations are private rights, in Indonesian law, different religious denominations can be brought before the law and found to be committing serious offenses. This may arouse suspicion, inter-group tension, persecution, and social violence. In this socio-legal case study, data were collected using interviews and documentation. Analyzing the trial process of the case allows us to conclude that the Public Court announced Shia teachings as the source of conflict. The court found the perpetrators guilty of blasphemy for teaching a doctrine which is different from the common Sunni belief. The conclusion is that the state is still weak in safeguarding and protecting the basic rights of religious minorities.