The President of Anjouan is the head of Anjouan, one of the three islands of the Union of Comoros. The position was firstly established in 1997 after the Declaration of independence of Anjouan. Secondly the position became President of the autonomous island of Anjouan following the adoption of the Union of Comoros Constitution of 2001.

The first President of Anjouan was Foundi Ibrahim Abdallah from 1997 to 1999.

Saïd Abeid Abdérémane succeeded to Foundi Ibrahim Abdallah in 1999 and was President of Anjouan until August 2001, date of the military putsch by Mohamed Bacar.

Mohamed Bacar held the elected position from 14 April 2002 to 26 April 2007, when the country's Federal Constitutional Court declared his remaining in office after his term ended on 14 April illegal. Two days later, Comorian president Ahmed Abdallah Sambi appointed Kaambi Houmadi as interim President of Anjouan. Houmadi was replaced by Dhoihirou Halidi on 11 May 2007. This solution was rejected by Bacar, who held his own illegal elections in June which, unsurprisingly, he won in a landslide result of massive fraud. In February 2008 the Government of the Union of Comoros declared it had failed to find a diplomatic solution to the crisis and organised an armed intervention on 25 March 2008 which quickly seized back control of the island. Ikililou Dhoinine, one of the federation's vice presidents, was appointed as interim leader of Anjouan on 26 March 2008. On 30 March, Lailizamane Abdou Cheik, who was head of Anjouan's Court of Appeal (and was therefore the constitutional successor to the Presidency in the event of a vacancy), was appointed as Interim President; he was sworn in on 31 March.^[1]

Following the presidential elections held in June 2008, Moussa Toybou was sworn in as president on 5 July 2008.

The takeover of Anjouan by the Government of the Union of Comoros has indeed transformed the statute of President of Anjouan into the statute of Governor with limited privileges.