Their SLAVES hailed from south of the Sahara.
Not their pharaohs.
At least one dynasty was from south of the Sahara. And there is always some admixture- miscegnation if you will- between ruling and slave populations. There is also what seems to be a sociobiological rule that the ruling class is lighter skinned than the subject population in every society with occasional anomalies i.e. the Ethiopian 25th dynasty that ruled Egypt.