Seretse Ian Khama retained the presidency in 2009, in elections that were deemed free and fair by electoral observers. Such relatively successful elections belie the homogenizing policy of the Botswana government that continues to impose the Tswana identity on all Botswana communities. As MRG reported in 2009, the chieftaincies based on Tswana identity deepen Tswana domination, while seriously undermining the identity, including religions, of other minorities. In the struggle against perceived Tswana privilege, Wayeyi and other minorities have appealed to the courts, as well as the ACHPR. What the government likes to portray as an ethnically homogeneous land is actually a multicultural country, with about 45 ethnic groups speaking about 26 different languages.

Minority rights advocacy organizations in Botswana continue to contest the constitutional provision that only eight ethnic groups are capable of nominating representatives to the House of Chiefs. Consequently, other groups, numbering over 36, feel that their language, culture and religions have come under threat because of the prevailing Tswana hegemony.

State resistance to an approach that is more respectful of minority rights was evident in Botswana's inaugural report to the ACHPR in November 2009. In his submission to the Commission, the Minister for Justice, Defence and Constitutional Affairs reported that the state had not implemented the court's decision of 2006 to allow the Basarwa tribe to return to the Central Kalahari Game Reserve (CKGR). He argued that the court's ruling presented 'impracticable solutions', but asserted that dialogue was ongoing between the state and the Basarwa community, to ensure that the community benefits from revenue from the park through creation of their own eco-tourism lodges within the CKGR. He said that Basarwa will be trained and allowed to run eco-lodges on condition that they desist from supporting game hunting. Meanwhile Survival International, a UK-based NGO, accused the Botswana government of issuing 112 mining licences on Basarwa land since their evictions, raising doubts about the government's intention to make the Basarwa co-owners in the mining and tourism wealth generated from CKGR. Such mining has been condemned as unethical by the Bench Marks Foundation, an ecumenical corporate accountability organization, the UN news agency IRIN reported in September 2009.

In March 2009, on a country mission to Botswana, James Anaya, UN Special Rapporteur on the rights and fundamental freedoms of indigenous peoples, witnessed how the exclusion of indigenous Basarwa and other minorities from 'the design and implementation of the Government development initiatives affecting them' affected the cultural diversity and identity of these communities. He observed that this approach ultimately impeded government programmes. Indeed, the present development paradigm on the part of the Botswana government runs counter to its own Framework for a Long-term Vision of Botswana (Vision 2016), which obliges the government to ensure the recognition of diversity and engage in the promotion of minority cultures.

In contrast to the lack of respect for ethnic diversity, the Botswana government has maintained a fairly liberal attitude towards religious diversity. According to the official website of the Botswana government, of the estimated 70 per cent of citizens who identify themselves as Christians, most are from the Anglican, Methodist and United Congregational Church of Southern Africa. These groups coexist with minority Christian groups such as Lutherans, Roman Catholics, the Church of Jesus Christ of Latter-day Saints (Mormons), Seventh-day Adventists, Jehovah's Witnesses, Baptists, the Dutch Reformed Church and Mennonites. Muslims, primarily of South Asian origin, who number slightly more than 5,000, as well as smaller groups of Hindus and Baha'is, enjoy equal treatment with other faiths. USCIRF reported that representatives of Baha'i, Christian, Hindu and Muslim communities came together in April 2009 to form and register an official interfaith council to discuss religious issues and promote interfaith dialogue.

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