During testimony at the International Criminal Tribunal for Rwanda (ICTR) investigating the 1994 Rwandan genocide, expert André Guichaoua referred to Butare as the "rebel province."
Because it had a large Tutsi minority, prefectural politics were dominated by the Parti Social Démocrate (PSD), rather than the Mouvement Républicain National pour la Démocratie et le développement (MRND), from which the genocidal Interahamwe drew recruits.
When the country erupted into bloodshed following the death of President Juvenal Habyarimana (no relation to the prefect) on 6 April 1994, Butare was untouched, with the notable exception of the Nyakizu commune.
Interim President Théodore Sindikubwabo, himself a native of Butare, appointed a new prefect on 19 April in a ceremony in the prefectural capital.
It has been suggested that the Hutu government leadership were particularly concerned about Butare because so many of them were natives; besides Sindikubwabo, Prime Minister Jean Kambanda (the first person convicted by the ICTR), General Augustin Ndindiliyimana (head of the Gendarmie), and Pauline Nyiramasuhuko, the minister of women and family affairs were all born in Butare.