On August 3, 1975, the late Bob Denard, with clandestine support from Jacques Foccart and the French government, removed president Ahmed Abdallah from office in an armed coup and replaced him with United National Front of the Comoros (UNF) member Prince Said Mohammed Jaffar. Just a few months later, in January 1976, Jaffar was ousted in favour of his Minister of Defence Ali Soilih. At this time, the population of Mayotte voted against independence from France in two separate referendums. The first, held in December 1974, won 63.8% support for maintaining ties with France, while the second, held in February 1976, confirmed that vote with an overwhelming 99.4%. The three remaining islands, ruled by President Soilih, instituted a number of socialist and isolationist policies that soon strained relations with France. On May 13, 1978, Bob Denard returned to overthrow President Soilih and re-instated Abdallah with the support of the French and South African governments. During Soilih's brief rule, he had faced seven additional coup attempts until he was finally forced from office and killed.

The islands of Anjouan and Mohéli declared their independence from the Comoros in 1997, in an attempt to restore French rule. France, however, rejected the islands' request, leading to bloody confrontations between federal troops and rebels. Colonel Azali Assoumani, Army Chief of Staff, seized power in a bloodless coup in April 1999, overthrowing the Interim President Tadjiddine Ben Said Massounde citing weak leadership in the face of the crisis. The BBC reported that Azali's takeover was the Comoros' eighteenth coup d'etat since independence in 1975. A subsequent failed attempt by Azali to consolidate power and re-establish control over the islands was the subject of international criticism, and the African Union, under the auspices of President Mbeki of South Africa, intervened, imposing sanctions on Anjouan to help broker negotiations and effect reconciliation. This involved introducing a new system of governmental autonomy for each island, plus a Union government for the three islands. Azali stepped down in 2002 to run in the democratic election of the President of the Comoro Union, which he won. Under ongoing international pressure, as a military ruler who had originally come to power by force and was not always democratic while in office, Azali led the Union through constitutional changes that enabled new elections.

The elections in 2006 were won by Ahmed Abdallah Mohamed Sambi, a Sunni Muslim Cleric  from Anjouan, nick-named the "Ayatollah" for his time spent studying Islam in Iran. Azali honoured the election results, thus allowing the first-ever peaceful and democratic exchange of power in the archipelagos' turbulent history. Iranian-trained Sunni Muslim cleric Ahmed Abdallah Mohamed Sambi,  won the May 2006 presidential election with 58% of the vote. Mr Sambi, a former MP, campaigned on promises to fight unemployment and corruption. He has dismissed charges from his opponents that he is an Islamic extremist.

The presidency of the union rotates between the three islands. The former incumbent, Azali Assoumani, represented Grande Comore. His successor is from Anjouan. A president from Moheli is set to take office in 2010. The presidents of the three semi-autonomous islands are vice presidents of the Union of Comoros. A 33-member national assembly sits on Grande Comore. However, a standoff developed between the federal government and Anjouan in June 2007, when Anjouan's leader, Mohamed Bacar, was re-elected in elections held in defiance of a central government order.

Colonel Mohamed Bacar (born May 5, 1962 in Barakani, Anjouan) was president of Anjouan, one of the three autonomous islands that make up the Union of the Comoros. He is a former chief of police on Anjouan and has studied extensively in France and the United States. He was part of a military coup on Anjouan in August 2001, and soon became the head of the country. He was elected by repressing the election and  became the first president of Anjouan in March 2002, in part due to his leading role in the separatist movement. On 26 April 2007, the country's Federal Constitutional Court proclaimed the presidency of Anjouan vacant, declaring Bacar's refusal to leave office after his term ended on 14 April illegal. Two days later, Comorian president Ahmed Abdallah Sambi made an agreement with the  Africa Union to force M. Bacar to vacate his office. Bacar then appointed M. DHOIHIROU Halidi as interim president of Anjouan.  In defiance of both the Union of Comoros government and the African Union (AU), Mohamed Bacar, 45, on 14 June 2007  inaugurated himself for a second term as the president of Anjouan Island. The Union government had withheld election material from Anjouan to try and prevent the poll from taking place, but Bacar printed his own ballot papers, went ahead with the vote on 10 June and claimed a landslide victory of 90 percent.

Currently there is great unrest in the Comores as Anjouan’s leader refuses to leave office despite the advice of the Comores President and the African Union. This week the Comores Government, representing Grand Comores and Moheli, with the support of the French in Mayotte, have begun recruiting ‘volunteers’ in Southern Africa and preparing air capacity for the removal of Bacar early in the New Year. The South African Government, whose President Thabo Mbeki has been so active representing the African Union in the Comores, is in a bit of a bind. The natural reservoir of ‘volunteers’ for the Comores mission, as well as the cargo aircraft for their transport, is located in South Africa and there has been a track record of successful intervention by South Africa in Comores affairs. The new law passed in South Africa outlawing the recruitment of such ‘volunteeers’, in pursuit of this mission is hampering an important South African foreign policy ambition.

It is also a problem for the French. While they are in favour of the ouster of Bacar their resources are thin on the ground. The major movement of their extra-governmental capacity into Ndjamena in Chad over the past three months, co-ordinated by the French paramilitary company ICS, has dried up much of the resources, manpower and air capability of the French. The 13th Parachute Dragoon Regiment, who do much of ‘extra-humanitarian work’ for the DGSE are heavily engaged in Chad and Djibouti and, despite the proximity to Mayotte, are not available in force to participate on their own. They, too, are looking to South Africa for assistance but the new South African legislation is hobbling them.