The Presbyterian Church in Rwanda (Église presbytérienne au Rwanda or EPR) is the second-oldest church in Rwanda. Established in 1907 by Ernst Johanssen and Gerhard Ruccius, two missionaries of the German-based Lutheran Missionary Society of Bethel, it was handed over to the Belgian Society of Protestant Missions in Congo in 1921, before being granted independence in 1959 under the name of the Evangelical Presbyterian Church in Rwanda. Held in suspicion and marginalised by the Catholic missionaries and the first generation of post-independence Rwandan leaders, it gained a certain form of recognition after Juvénal Habyarimana became president in 1973, which explains why many Presbyterian church leaders, including the president, Michel Twagirayesu, showed unfettered loyalty to the regime before and during the genocide.

Like the Catholic Church, the Presbyterian Church emerged from the genocide bruised and disoriented with nearly 20 per cent of its pastors assassinated, its infrastructure damaged or destroyed and about a quarter of its members in refugee camps in Zaire or elsewhere. However, the manner in which the church reconstructed itself after the tragedy differs from that of the Catholic Church in several respects. The Catholic Church in Rwanda, because of its size and its incorporation into a centralised international body, retained its structure and its integrity after the genocide despite the assassination of three bishops in June 1994. The priests who took refuge in Goma or further afield in July 1994 rapidly lost influence. The bishops remained in Rwanda with the exception of Phocas Nikwigize, who left Ruhengeri for Goma in July 1994 and was allegedly killed by the RPF two years later at the border. Meanwhile, the Catholic Church in Rwanda was divided on the issue of genocide, with some openly recognising the church's failure to denounce the systematic extermination of the Tutsi people and others adopting a defensive attitude and focusing all their attention on the shortcomings of the new government. As we shall see in subsequent chapters, the two groups found some common ground in the late 1990s, but the uneasiness with regard to the genocide against the Tutsi remains up to this day.