Northern Africa was once part of the Roman Empire. Because Christianity became the state religion around 300, it propagated to all areas of the Empire. But as the Western Empire declined, the cultural vacuum left behind allowed for competing philosophies to take root. By the 700's, Islam had begun to spread into African areas that had been wholly Christian, and then even moved into Spain.
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One important factor is that Islam spread the written word much farther than before, as well as more accurate methods of measurement and weight. By educating with these methods and showing how they made trade both accurate and honest, the religion was given a foothold it might not have had otherwise.
Let us not forget that Islam is a missionary religion as well, and part of the religious requirements of being a Muslim is to be involved in the propogation of faith. Just as we have seen a growth in the Christian church in N. Africa, similarly it could be argued that we have seen a growth of Islam in other parts of the world.
This is a great question and one of reasons why Christianity spread at least is because of the effort of Christian missionaries. In the past England sent many missionaries to Africa. In more recent times, the United States and South Korea have sent thousands of missionaries. Due to their efforts there has been great growth in the African church.
Another point that is important to realize is that Christianity is a missionary religion. Therefore, when the Africans started their own churches, they started a mission as well. For these to reasons, the church has grown tremendously.
Today, most Africans are either Christians or Muslims. The reason is largely due to colonialism. If you look at it on a map, the northern part of Africa is mostly Islamic, including the northeast. The southern portion of Africa is mostly Christian, on the other hand.