Mamilla cemetery was one of the largest and most important Muslim cemeteries in Jerusalem. The plans to build a “Museum of Tolerance” in it led to heated protests and a prolonged legal procedure in Israel’s Supreme Court of Justice. In 2008, the court approved the plans and many hundreds of graves were exhumed. Through the available sources, including the court’s archival files, we discuss political, legal, and archaeological aspects of this case, focusing on ethics about cemeteries and descendant communities. The discussion shows that the Israel Antiquities Authority breached the court orders and that the treatment of the archaeological remains was biased. “Their” graves were destroyed, and the bones reburied in secret, while “our” remains in the same areas were carefully excavated and preserved. Tolerance to “our” heritage at the expense of “theirs” is intolerance.