What were the causes for genocide in Rwanda in the 1990s?

The Rwandan genocide was ethnically motivated. This being said, it was a civil war between the two ethnic groups in Rwanda: The Hutu's, who made up 85% of the population, and the Tutsi, that made up 14%. Belgian and German colonists who ultimately had more control over the citizens encouraged a two class system that favored the Tutsi far more than it did the Hutu. The Tutsi were given Western styles of education and what not, which made them privileged.

Around the 1950's is where the Hutu started their rebellion against the system that saw them as second class citizens. By the time the Belgian colonist withdrew, the Hutu, being the majority had total control of the country. Throughout the 1960's the Tutsi were massacred.

tl; dr racial discrimination rooting back 100's of years, systematic oppression.