A former schoolteacher accused of participating in the mass genocide in Rwanda pleaded not guilty as his war crimes trial began Monday.

Jacques Mungwarere, 39, is the second Rwandan to be prosecuted under Canada's Crimes Against Humanity and War Crimes Act, which was introduced in 2000 and allows for prosecution no matter where or when an alleged war crime may have been committed.

Jacques Mungwarere, 39, is accused of leading or participating in massacres in two churches and a hospital in Kibuye. (Laurie Foster-MacLeod/CBC)

Mungwaware, arrested in 2009 in Windsor, Ont., has opted for a trial by judge only.

He sat behind his legal team in court, listening as prosecutors laid out their case to a judge at an Ottawa courtroom Monday.

The prosecution said it would call upon several witnesses who claim they saw Mungwawere take part in an attack on a hospital where Tutsis had sought shelter.

Genocide expert called as first witness

The trial opened with testimony from professor Timothy Paul Longman, who lived in Rwanda before 1994 and spent years studying its ethnic and political divisions.

He explained the historic divide between Rwanda's minority Tutsi population and the majority Hutu people and how those differences became more entrenched during the era of European colonialism.

Longman, who also served in the country with Human Rights Watch after the genocide, spoke about the court system set up in Rwanda in the years following the genocide to try people accused of taking part in the killings. Rwandan genocide expert Timothy Longman testified Monday at the war crimes trial of former schoolteacher Jacques Mungwarere. (Court sketch by Laurie Foster-McLeod/CBC )

Defence lawyer Marc Nerenberg asked Longman whether some of those charged with crimes were victims of false accusations.

Longman told court that has happened, but added that there have been cases where people making false claims have themselves ended up in jail.

Massacres at churches, hospital

Rwandan officials allege Mungwarere led or participated in mass killings of civilians, including notorious massacres in two churches and a hospital in Kibuye.

In all, nearly 800,000 members of Rwanda's Tutsi minority and moderates from the Hutu majority were killed during a 100-day period of the Rwandan genocide.

The first person prosecuted under the act is Desire Munyaneza, who was sentenced to life in prison in 2009.

With files from the CBC's Tom Perry