"We are sorry if you get woken up by the Muslim call to prayer in the morning." Those were some of the first words I heard at my hotel when I arrived in Addis Ababa, on my first trip to Ethiopia. I confess - I was a bit confused. Call to prayer? In the capital of a "Christian country in a sea of Muslims", as Ethiopia is sometimes called? Perhaps I was in a Muslim quarter of Addis Ababa that had been recently established?

No, the situation was far more complicated than that, and one about which I had a surprisingly limited awareness. Most non-Ethiopians, including the immediate neighbours of Ethiopia, also believe that Ethiopia is predominantly Christian. The more sophisticated might believe that there is a Muslim minority - and it was to learn about that population that drew me to Ethiopia in the first place. But it is not a minority. About 55 per cent of Ethiopia's parliament is Muslim and representatives from the country's Islamic community insist they are at least 50 per cent of the population. While the US State Department estimates that this number is a bit lower, Islam might actually be the religion with the most adherents in Ethiopia.

If there is any "Muslim quarter" in Addis, it must be an old one. Christianity was the first religion to arrive in Ethiopia - but only in the north of the country. Where the capital, Addis Ababa, is located, the area of Shawa, was the domain of a Muslim sultanate in the early 8th century. Most historical narratives portray Ethiopia's as a Christian story. If Islam is even mentioned, it is associated with disconnected tribesman in the lowlands who battled Christian kingdoms in the highlands. But history is written by the powerful and now academics are rediscovering the Muslim history of this country of such noble heritage.

As I met people from Ethiopia's Muslim community, I was struck by their diversity. Most Ethiopian Muslims are influenced by Sufism, and follow the same Sunni rites as their neighbours in Yemen, Somalia and Djibouti (the Shafi'i rite) - but there are also adherents of other Sunni rites, and a significant Salafi movement within Ethiopia. There are dozens of ethnic and linguistic groups among Muslim Ethiopians, from all areas of the country.

But what they share is a long history of discrimination against them. Early Christian-Muslims relations in Ethiopia were very good - the Prophet of Islam sent several Muslim refugees to live among Christians in Ethiopia, who had a very high opinion of the king at that time, who later became Muslim. In the medieval era, Christian Ethiopians under the Zagwes refused to be drawn into the European crusades against the Muslim world, which led to Saladin giving the Ethiopian Orthodox Church a monastery in Jerusalem. In the same era, Muslims and Christians lived in separate kingdoms and sultanates in Ethiopia, but in peaceful coexistence - and their example proves that deeply religious and pious people of different religions need not be at war with one another.

But with the rise of the Solomonic dynasty in 1270 that came to an end. That dynasty, like many others of its age, was expansionist and aggressive, leading to a great number of conflicts with Muslim sultanates over a period of hundreds of years in Ethiopia. The length of the Solomonic dynasty is staggering - Haile Selassie was its last Emperor, and his reign ended in 1974. He saw the establishment of a modern Ethiopia, but not a modern educational system - at least, not for Muslim Ethiopians. The historians and educators I interviewed in Ethiopia bemoaned the standard of education among Muslim Ethiopians, explaining to me that during Haile Selassie's tenure, Muslim regions did not receive the same attention as Christian regions and few modern educational institutions were established. Haile Selassie had a formula for Ethiopia: one country, one people, one religion. Muslims were not part of that equation. The revolutionary regime that overthrew Haile Selassie, the Derg, introduced education for all, but as a communist movement, Muslim communities still suffered discrimination.

Many of those whom I met were from that generation - a generation that had access to education, and began to learn about their religion in a modern sense. With the establishment of a more democratic constitution in 1994, Muslim Ethiopians began to try to build more institutions for themselves.

Much of the contemporary analysis surrounding Ethiopia's relationship with the Muslim world revolves around Somalia, and Ethiopia's invasion of that country in 2006. I saw quite a different face, however, to the nation. I saw a huge number of Muslims speaking excellent Arabic (perhaps more than any non-Arabic speaking country I had ever been to), proud of the history of this ancient land that had never been conquered. On the other hand, I also saw the sadness of many Muslim Ethiopians, who were frustrated that while rich Muslim countries might provide funds to build mosques, or provide food during Ramadan, they would not contribute to provide for the institutions needed to improve the capacity of this thriving community. And it's not hard to see why - many simply do not believe there is a community there to support in the first place.

But there is an Ethiopian Muslim community there: a community that has learnt to thrive against the odds, and one that teaches lessons about identity in a diverse society and the role of religion in the modern world. It is a community that deserves to be known.

H A Hellyer is a Fellow of the Centre for Research in Ethnic Relations at the University of Warwick, UK, and director of the Visionary Consultants Group.