The first human inhabitants of the Comoro Islands are thought to have been African and Austronesian settlers, traveling by boat. They settled there no later than the sixth century AD, the date of the earliest known archaeological site, found on Nzwani, though some sources speculate that settlement began as early as the first century. The islands of Comoros became populated by a succession of diverse groups from the coast of Africa, the Persian Gulf, the Malay Archipelago, and Madagascar. Swahili settlers first reached the islands as a part of the greater Bantu expansion that took place in Africa throughout the first millennium.
Development of the Comoros is periodized into phases, beginning with Swahili influence and settlement in the Dembeni phase (ninth to tenth centuries), during which each island maintained a single, central village. From the eleventh to the fifteenth centuries, trade with the island of Madagascar and merchants from the Middle East flourished, smaller villages emerged, and existing towns expanded. The citizens and historians of the Comoros state that early Arab settlements date to even before their known arrival to the archipelago, and Swahili historians frequently trace genealogies back to Arab ancestors who had traveled from Yemen and the ancient kingdom of Saba' in Eden (thought to be the biblical Eden), even though people are unsure if this is true.

Arab Colonization
Arab merchants first brought Arab Islamic influence to the islands. One most likely fact is that Arabs traded for slaves in Africa, increasing the spread and dominance of Arab culture. As their religion gained hold, large mosques were constructed. The Comoro Islands, like other coastal areas in the region, were important stops in early Islamic trade routes frequented by Persians and Arabs. Despite its distance from the coast, Comoros is situated along the major sea route between Kilwa and Mozambique, an outlet for Zimbabwean gold.
The Shirazi people traded along the coasts of East Africa, and the Middle East, establishing settlements and colonies in the archipelago.
Arab colonization in the region increased when nearby Zanzibar fell to Arab Omani rule, and Comorian culture, especially architecture and religion, also increasingly came under Arab imperial sway. Many rival sultanates colonized the area in the sixteenth and seventeenth centuries.
By the time Europeans showed interest in the Comoros, the dominant Arab cultural veneer of the islands led many to remind of the society's Arab colonial history at the expense of its native Swahili and African heritage. More recent western scholarship by Thomas Spear and Randall Pouwells emphasizes black African historical predominance over the diffusionist perspective.

European Contact and French Colonization
Portuguese explorers first visited the archipelago in 1505.
In 1793, Malagasy warriors from Madagascar first started raiding the islands for slaves, and later settled and seized control in many locations. France first established colonial rule in the Comoros in 1841. The first French colonists landed in Mayotte, and Andrian Tsouli, the Malagasy King of Mayotte, signed the Treaty of April 1841, which ceded the island to the French authorities.
In 1886, Mohéli was placed under French protection by its Queen Salima Machimba. That same year, after consolidating his authority over all of Grande Comore, Sultan Said Ali agreed to French protection of his island, though he retained sovereignty until 1909. Also in 1909, Sultan Said Muhamed of Anjouan abdicated in favor of French rule. The Comoros (or Les Comores) was officially made a French colony in 1912, and the islands were placed under the administration of the French colonial governor general of Madagascar in 1914.
The Comoros served as a way station for merchants sailing to the Far East and India until the opening of the Suez Canal significantly reduced traffic passing through the Mozambique Channel. The native commodities exported by the Comoros were coconuts, cattle and tortoiseshell. French settlers, French-owned companies, and wealthy Arab merchants established a plantation-based economy that now uses about one-third of the land for export crops. After its annexation, France converted Mayotte into a sugar plantation colony. The other islands were soon transformed as well, and the major crops of ylang-ylang, vanilla, coffee, cocoa bean, and sisal were introduced.
Agreement was reached with France in 1973 for Comoros to become independent in 1978. The deputies of Mayotte abstained. Referenda were held on all four of the islands. Three voted for independence by large margins, while Mayotte voted against, and remains under French administration. On July 6, 1975, however, the Comorian parliament passed a unilateral resolution declaring independence. Ahmed Abdallah proclaimed the independence of the Comorian State (État comorien; ???? ?????) and became its first president.

Independence
The next 30 years were a period of political turmoil. On 3 August 1975, mercenary 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. Months later, in January 1976, Jaffar was ousted in favor of his Minister of Defense Ali Soilih.
At this time, the population of Mayotte voted against independence from France in two 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 13 May 1978, Bob Denard returned to overthrow President Soilih and reinstate Abdallah with the support of the French and South African governments. During Soilih's brief rule, he faced seven additional coup attempts until he was finally forced from office and killed.
In contrast to Soilih, Abdallah's presidency was marked by authoritarian rule and increased adherence to traditional Islam and the country was renamed the Federal and Islamic Republic of Comoros (République Fédérale Islamique des Comores; ??????? ????? ????????? ????????? ). Abdallah continued as president until 1989 when, fearing a probable coup d'état, he signed a decree ordering the Presidential Guard, led by Bob Denard, to disarm the armed forces. Shortly after the signing of the decree, Abdallah was allegedly shot dead in his office by a disgruntled military officer, though later sources claim an antitank missile was launched into his bedroom and killed him. Although Denard was also injured, it is suspected that Abdallah's killer was a soldier under his command.
A few days later, Bob Denard was evacuated to South Africa by French paratroopers. Said Mohamed Djohar, Soilih's older half-brother, then became president, and served until September 1995, when Bob Denard returned and attempted another coup. This time France intervened with paratroopers and forced Denard to surrender. The French removed Djohar to Reunion, and the Paris-backed Mohamed Taki Abdulkarim became president by election. He led the country from 1996, during a time of labor crises, government suppression, and secessionist conflicts, until his death November 1998. He was succeeded by Interim President Tadjidine Ben Said Massounde.
The islands of Anjouan and Mohéli declared their independence from the Comoros in 1997, in an attempt to restore French rule. But France rejected their request, leading to bloody confrontations between federal troops and rebels. In April 1999, Colonel Azali Assoumani, Army Chief of Staff, seized power in a bloodless coup, overthrowing the Interim President Massounde, citing weak leadership in the face of the crisis. This was the Comoros' 18th coup d'état since independence in 1975. Azali, however, failed to consolidate power and reestablish control over the islands, which was the subject of international criticism. The African Union, under the auspices of President Thabo Mbeki of South Africa, imposed sanctions on Anjouan to help broker negotiations and effect reconciliation. The official name of the country was changed to the Union of the Comoros and a new system of political autonomy was instituted for each island, plus a union government for the three islands was added.
Azali stepped down in 2002 to run in the democratic election of the President of the Comoros, 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 Comoros through constitutional changes that enabled new elections. A Loi des compétences law was passed in early 2005 that defines the responsibilities of each governmental body, and is in the process of implementation. The elections in 2006 were won by Ahmed Abdallah Mohamed Sambi, a Sunni Muslim cleric nicknamed the "Ayatollah" for his time spent studying Islam in Iran. Azali honored the election results, thus allowing the first peaceful and democratic exchange of power for the archipelago.
Colonel Mohammed Bacar, a French-trained former gendarme, seized power as President in Anjouan in 2001. He staged a vote in June 2007 to confirm his leadership that was rejected as illegal by the Comoros federal government and the African Union. On March 25, 2008 hundreds of soldiers from the African Union and Comoros seized rebel-held Anjouan, generally welcomed by the population: there have been reports of hundreds, if not thousands, of people tortured during Bacar’s tenure. Some rebels were killed and injured, but there are no official figures. At least 11 civilians were wounded. Some officials were imprisoned. Bacar fled in a speedboat to the French Indian Ocean territory of Mayotte to seek asylum. Anti-French protests followed in Comoros (see 2008 invasion of Anjouan). Since independence from France, the Comoros experienced more than 20 coups or attempted coups.