The earliest evidence we have for religious faith in Africa is from Blombos Cave in South Africa, where people may have been using red ochre for funerals about 100,000 years ago. Around 6000 BC, people put up standing stones in East Africa (modern Sudan), maybe marking the changing seasons.
Polytheism triumphed when Akhenaten died, though, and survived through the conquest of North Africa by the Phoenicians who introduced their own gods to North Africa, like the goddess Tanit and the god Ba’al. The Greeks, and then the Romans, soon added their gods to the gods worshipped in North Africa.
Around 300 AD there was a second great change in African religious belief when many North and East Africans gradually followed the Roman Emperor’s lead in converting to the monotheistic faith of Christianity. The great Christian theologian St. Augustine was from North Africa. By the 500s AD Christianity won over most of North Africa, including Egypt, and also the kingdom of Axum south of Egypt (modern Sudan, Eretria, and Ethiopia). The Christians of North Africa were split among the Donatists, the Catholics, and then the Vandal Arians.
In this same time period, the Bantu were gradually expanding across southern Africa, bringing their faith with them. Bantu faith continued to de-emphasize polytheism, while having instead a firm belief in ghosts and their power over living people. Some of these ghosts were your own dead parents or grandparents. Others might be the ghost of a dead king or hero, and these might be remembered for a long time, rather like Christian saints.
In the late 600s AD, another monotheistic faith, Islam, came to Africa, first across the Red Sea to Somalia, then Egypt and then spreading rapidly across North Africa. A hundred years later, almost the entire population of North Africa had converted to Islam. Islam quickly spread across the Sahara Desert as well, so that many people of the Sudan, the grasslands south of the Sahara, became Muslims too. All the way south to the great rain forests, there were many Muslims or people who followed at least some Muslim beliefs. And, thanks to Arab and Indian traders, the entire east coast of Africa became Muslim, as far south as Mozambique. Ethiopia, however, remained Christian.
South of the rain forests, however, in central and western Africa, Bantu religion remained dominant. In the Kalahari desert, the San people kept up their own faith, which was very similar to the Bantu faith in its emphasis on ancestor ghosts.
Bibliography and further reading about African religion:
Myths and Legends of Ancient Egypt, by Thomas James (1971)
Children of the Lamp (Akhenaten Adventure), by P. B. Kerr (2004)
Abiyoyo, by Pete Seeger (reprinted 1994)
A Coalition of Lions, by Elizabeth E. Wein (2003) – A novel about Christian Africa in the 500s AD- warning: this book is the second in a series!
African Religion, by Aloysius Muzzanganda Lugira, Paula R. Hartz (2004)
The Atlas of Islam: People, Daily Life and Traditions, by Neil Morris, Manuela Cappon, Gian Paulo Faleschini, Studio Stalio (2003)