Rwandan Genocide

In 1994 Hutu rulers managed to slaughter somewhere between 500,000 and 1,000,000 of their fellow Rwandans who were of the Tutsi persuasion in only 100 days.  This eliminated approximately 20% of the Rwandan population and 70% of the Tutsi population minority.

The Tutsi held power for centuries before Rwanda became colonized by Germany then Belgium after Germany lost WWI.

 The Catholic Church, wishing to convert the country to Catholicism developed a strategy to target the ruling elite Tutsi for conversion.  The Tutsi did not take well to converting but tolerated the Church due to the positive financial influence the provided to the country.  The Church wished to avoid conflict so they made sure to appease the ruling class.  

A Rwandan refugee girl stares at a mass grave where dozens of bodies have
been laid to rest July 20, 1994. Rwandan refugees who escaped from fighting
between government troops and RPF rebels are dying by the hundreds of
dehydration, lack of food and cholera.

The Hutu were more susceptible to conversion and because of this Rwanda became one of the most Christian regions in all of Africa.

Eventually, the Catholic Church, growing tired of failing at converting the Tutsi, began to back the Hutu population and began leading them to what was ultimately a successful revolution against the ruling Tutsi elite. 

The civil war that followed ultimately lead to the largely Christian Hutu population conducting an extermination campaign against the Tutsi.  

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Learn More: 
Wikipedia
United to End Genocide:  Rwanda
Rwanda Genocide Timeline: About Education