Little is known of the first inhabitants of the archipelago, although a sixth-century settlement has been uncovered on Nzwani by archaeologists. Historians speculated that Indonesian immigrants used the islands as stepping stones on the way to Madagascar prior to A.D. 1000. Because Comoros lay at the juncture of African, Malayo-Indonesian, and Arab spheres of influence, the present population reflects a blend of these elements in its physical characteristics, language, culture, social structure, and religion. Local legend cites the first settlement of the archipelago by two families from Arabia after the death of Solomon. Legend also tells of a Persian king, Husain ibn Ali, who established a settlement on Comoros around the beginning of the eleventh century. Bantu peoples apparently moved to Comoros before the fourteenth century, principally from the coast of what is now southern Mozambique; on the island of Nzwani they apparently encountered an earlier group of inhabitants, a Malayo-Indonesian people. A number of chieftains bearing African titles established settlements on Njazidja and Nzwani, and by the fifteenth century they probably had contact with Arab merchants and traders who brought the Islamic faith to the islands.

A watershed in the history of the islands was the arrival of the Shirazi Arabs in the fifteenth and sixteenth centuries. The Shirazi, who originated from the city of Shiraz in what is now Iran, were Sunni (see Glossary) Muslims adhering to the legal school of Muhammad ibn Idris ash Shafii, an eighth-century Meccan scholar who followed a middle path in combining tradition and independent judgment in legal matters. The Shirazi Arabs traveled and traded up and down the East African coast and as far east as India and Maldives. A legend is recounted on Comoros and on the East African coast of seven Shirazi brothers who set sail in seven ships, landed on the coast of northwest Madagascar and on Njazidja and Nzwani, and established colonies in the fifteenth century. The Shirazi, who divided Njazidja into eleven sultanates and Nzwani into two, extended their rule to Mahoré and Mwali, although the latter in the nineteenth century came under the control of Malagasy rulers. The Shirazi built mosques and established Islam as the religion of the islands. They also introduced stone architecture, carpentry, cotton weaving, the cultivation of a number of fruits, and the Persian solar calendar. By the sixteenth century, the Comoros had become a center of regional trade, exporting rice, ambergris, spices, and slaves to ports in East Africa and the Middle East in exchange for opium, cotton cloth, and other items.

The first Europeans to visit the islands were the Portuguese, who landed on Njazidja around 1505. The islands first appear on a European map in 1527, that of Portuguese cartographer Diogo Roberos. Dutch sixteenth-century accounts describe the Comoros sultanates as prosperous trade centers with the African coast and Madagascar. Intense competition for this trade, and, increasingly, for European commerce, resulted in constant warfare among the sultanates, a situation that persisted until the French occupation. The sultans of Njazidja only occasionally recognized the supremacy of one of their number as tibe, or supreme ruler.

By the early seventeenth century, slaves had become Comoros' most important export commodity, although the market for the islands' other products also continued to expand, mainly in response to the growing European presence in the region. To meet this increased demand, the sultans began using slave labor themselves, following common practice along the East African coast.

Beginning in 1785, the Sakalava of the west coast of Madagascar began slaving raids on Comoros. They captured thousands of inhabitants and carried them off in outrigger canoes to be sold in French-occupied Madagascar, Mauritius, or Reunion to work on the sugar plantations, many of which French investors owned. The island of Mahoré, closest of the group to Madagascar, was virtually depopulated. Comoran pleas for aid from the French and the other European powers went unanswered, and the raids ceased only after the Sakalava kingdoms were conquered by the Merina of Madagascar's central highlands. After the Merina conquest, groups of Sakalava and Betsimisaraka peoples left Madagascar and settled on Mahoré and Mwali.

Prosperity was restored as Comoran traders again became involved in transporting slaves from the East African coast to Reunion and Madagascar. Dhows carrying slaves brought in huge profits for their investors. On Comoros, it was estimated in 1865 that as much as 40 percent of the population consisted of slaves. For the elite, owning a large number of slaves to perform fieldwork and household service was a mark of status. On the eve of the French occupation, Comoran society consisted of three classes: the elite of the Shirazi sultans and their families, a middle class of free persons or commoners, and a slave class consisting of those who had been brought from the African coast or their descendants.

Data as of August 1994