A new law criminalizing 'genocidal ideology' was promulgated on 1 October 2008 and began to be implemented in 2009. The terms of the crime are ambiguously expressed; however, the offence is punishable by 10 to 25 years' imprisonment. The intention of this law has been questioned by many international organizations, including the NGO Article 19. It is feared that the law is an instrument for stifling freedom of expression and limiting political space for those opposed to the current government. In December 2009, Rwandan opposition presidential candidate Bernard Ntaganda was summoned to answer charges under the law at a Senate committee inquiry. He denied promoting genocide ideology and ethnic 'divisionism'. While government sensitivities to the use of ethnic differences are understandable given the 1994 genocide perpetrated against the Tutsi minority, the state's ethnic policy may also conceal hierarchies and discrimination against vulnerable minorities such as the Batwa and women from minority groups.

While Rwanda's 1994 conflict pitted the Hutu and Tutsi ethnic groups against each other, MRG has reported that Rwanda's minority Batwa population also suffered mass killings. But they were not recognized in post-conflict reparations frameworks in Rwanda. In May 2009 the UN Human Rights Committee, in its concluding observations on Rwanda's Periodic Report, raised concerns about the non-recognition of the existence of minorities and indigenous peoples in Rwanda, as well as reports that members of the Batwa community are victims of marginalization and discrimination.

Rwanda's religious minorities have also suffered some discrimination. USCIRF reported in 2009 that members of Jehovah's Witnesses continued to be detained by local authorities. Seventeen were arrested and imprisoned for up to one week after they declined, for religious reasons, to participate in night patrols – a community policing response to crime. However, judges ruled in 2005 that members of the faith were not required by any law to take part in the patrols.

Government officials presiding over wedding ceremonies generally require couples to take an oath while touching the national flag. Jehovah's Witnesses object to this on religious grounds, making it difficult for its members to marry legally. Some find placing their hands on a Bible on top of the flag is an acceptable alternative.

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