Rwanda's most wanted genocide fugitive has been arrested in South Africa after three decades on the run.

A collaborative operation by the International Residual Mechanism for Criminal Tribunals (IRMCT), the Fugitive Tracking Team and South African authorities resulted in the arrest of Fulgence Kayishema, 63, on Wednesday afternoon in Paarl, Western Cape.

It had been known for years that Kayishema, who once worked as a bouncer, was hiding in South Africa. 

However, fractured relations between South Africa and Rwanda made it difficult to track and arrest him.

IRMCT Chief Prosecutor, Serge Brammertz, said President Cyril Ramaphosa and government arms played a big role in the team's effort to arrest Kayishema.

"The thorough investigation that led to this arrest was made possible through the support and cooperation of the Republic of South Africa and the Operational Task Team established by President Ramaphosa to assist our Fugitive Tracking Team."

He added:

My office would like to recognise, in particular, the Directorate of Priority Crimes Investigations, Crime Intelligence Western Cape Province, SAPS Interpol, and the Ministry of Home Affairs. Their exceptional skills, rigour and cooperation were critical for this success.

In close collaboration with numerous national law enforcement and immigration organisations, the investigation that resulted in Kayishema's detention included many nations.

Kayishema used a variety of aliases and fake documents to hide his name and location while evading the law.

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He also relied on a network of reliable allies, including family, ex-members of the Rwandan Armed Forces and the Rwandan Democratic Forces of Liberation, and individuals who shared the murderous Hutu Power ideology.

Through an analysis-driven inquiry that used multi-source evidence and both conventional and cutting-edge methodologies, Kayishema was found and apprehended, the IRMCT said.

There was also the close involvement of Mozambique and Eswatini in tracking down the Rwandan fugitive.

"We also received vital support from similar task forces in other African countries, notably the Kingdom of Eswatini and the Republic of Mozambique," he added.

"Rwandan authorities under the leadership of Prosecutor General Aimable Havugiyaremye continued to be our strongest partners and provided essential assistance."

Rwandan president Paul Kagame has pushed for all genocide enablers to be brought to book.

Kayishema was charged with genocide, complicity in genocide, conspiracy to commit genocide and crimes against humanity by the International Criminal Tribunal for Rwanda (ICTR) in 2001 for killings and other crimes committed in Kivumu Commune, Kibuye Prefecture, during the 1994 genocide against the Tutsi in Rwanda.

According to the accusation, on 15 April 1994, at the Nyange Church in Kivumu commune, Kayishema and other co-defendants killed more than 2 000 refugees, including men, women, elderly people, and young children.

Kayishema allegedly took an active role in the preparation and execution of this atrocity, purchasing and distributing petrol to burn down the church that housed the refugees, among other things.

When it didn't work, Kayishema and others used a bulldozer to destroy the church, killing and burying the refugees inside.

Strained relations with South Africa

Relations between South Africa and Rwanda hit a bad patch when reports surfaced that Kagame was allegedly hunting down his enemies in South Africa without involving local authorities.

The 2014 assassination of the former chief of intelligence for Rwanda, Patrick Karegeya who was in exile in South Africa, was the highest strain point between the two countries.

Karegeya was found dead in his hotel room on 1 January 2014.

Michela Wrong’s book, Do Not Disturb: The Story of a Political Murder and an African Regime Gone Bad, claims Karegeya was killed by a Rwandan government hitman named "Apollo".

However, in court papers filed by Karegeya's family for an inquest into his death, there's mention of four Rwandan suspects.

Even before Karegeya's assassination, Rwandan fugitives had been meeting similar fates in South Africa.

One of them was Rwanda's former army chief of staff, General Kayumba Nyamwasa who survived an attempt on his life in 2010.

SA agrees to help

Brammertz in 2019 briefed the United Nations Security Council that South Africa was not cooperating in the hunt for Kayishema.

"Since 2018, this investigation has been significantly impeded by challenges in obtaining cooperation from South Africa."

But last year, having registered breakthroughs in tracking down some of the fugitives, particularly Protais Mpiranya who was tracked down to a grave in Harare, Zimbabwe, there have been more scores for the IRMCT.

Last May, IRMCT went to Pretoria and Cape Town after South Africa agreed to work with them through an operational interdepartmental investigative team in tracking Kayishema.

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