"Yesterday afternoon, Fulgence Kayishema, one of the world's most wanted genocide fugitives, was arrested in Paarl, South Africa in a joint operation," the International Residual Mechanism for Criminal Tribunals (MICT) said in a statement.
Around 800,000 Rwandans, most of them ethnic Tutsis, were slaughtered over 100 days at the hands of Hutu extremists.
He and others allegedly murdered more than 2,000 Tutsi men, women and children who had taken refuge in a Catholic church in Nyange in Kivumu district.
"Kayishema directly participated in the planning and execution of this massacre, including by procuring and distributing petrol to burn down the church with the refugees inside," the statement said. "When this failed, Kayishema and others used a bulldozer to collapse the church, burying and killing the refugees inside. Kayishema and others then supervised the transfer of corpses from the church grounds into mass graves."
The MICT in 2015 took over the work of the International Criminal Tribunal for Rwanda (ICTR), which the United Nations had set up following the genocide.
Kayishema's arrest was carried out in a joint operation by MICT's Fugitive Tracking Team and the South African authorities, the statement said. The investigation "spanned multiple countries across Africa and elsewhere, in strong cooperation with many national law enforcement and immigration agencies."
During his flight from justice, Kayishema used many aliases and false documents and relied on a "network of trusted supporters", the statement disclosed. These included family members, members of the former Rwandan armed forces, the Democratic Forces for the Liberation of Rwanda (FDLR) rebel group "and those aligned with the genocidal Hutu Power ideology".
MICT Chief Prosecutor Serge Brammertz paid tribute to "the exceptional skills, rigour and cooperation" of South African investigators and singled out Eswatini and Mozambique for their help.
Kayishema "will finally face justice for his alleged crimes [...]. This arrest is a tangible demonstration that this commitment does not fade and that justice will be done, no matter how long it takes," he said, highlighting that "genocide is the most serious crime known to humankind."
Naphtali Ahishakiye, executive secretary of Ibuka, an umbrella association of genocide survivors, said the arrest "sends a strong message to other fugitives and masterminds of the 1994 genocide [..] that they can never evade justice forever."
The three other fugitives on the wanted list also face multiple charges of genocide and crimes against humanity: Aloys Ndimbati; Charles Ryandikayo; and Charles Sikubwabo.
The ICTR court sentenced 62 people, including a 30-year term handed to former minister Augustin Ngirabatware, and acquitted 14. It closed in late 2015, handing over to the MICT to pursue cases against suspects.
In September 2022, one of Rwanda's richest men before the genocide, Felicien Kabuga, who moved to France under a false identity, went on trial in The Hague. His trial was put on hold in March amid concerns over his health.
Ahishakiye pointed to the problems in getting Kabuga on trial to stress the need for timely justice.
"Our wish is that he [Kayeshima] is extradited to Rwanda for his trial so that he can answer directly to the people whose crimes affected," he told AFP, adding: "We hope that his trial is expedited, and that the wheels of justice do not entertain the sorts of delays that the Kabuga trial has experienced."
Rwanda started trying genocide suspects in 1996, and on a single day in April 1998 had 22 of them executed by firing squad. It abolished the death penalty in 2007, lifting the main obstacle for the ICTR to extradite genocide suspects to Rwanda for trial.
Between 2005 and 2012, more than 12,000 "gacaca" community-based courts put nearly two million people on trial and convicted 65 percent, sending most to prison.
Other convictions have been handed down in the former colonial power Belgium as well as in France, Sweden, Finland, Norway, Germany, the Netherlands, the United States and Canada.
But three other prominent fugitives -- Augustin Bizimana, Protais Mpiranya and Pheneas Munyarugarama -- all died without facing justice.