I think that the answer that you are looking for is to be found on the second page of the chapter -- p. 377 in my copy. What Diamond is saying is that we tend to think of Africans as a bunch of homogeneous black people when in fact there are many different kinds of people in Africa.
Diamond argues that whites (up in the north) and blacks were both native to Africa. Also, however, he points out that there are two other groups of continental Africans that are not physically similar to blacks. These are the pygmies and the Khoisan. Finally, he says that there are Indonesians who are native to the island of Madagascar.
Because of all this diversity, it is incorrect for us to think of Africans as all being black (and that's without even talking about the diversity of people who we would call black).