One view:
He created human beings in his own image, in the land of Africa. Science says that life originated from Africa. With the changing of lands shifting people in the north and south grew paler, and people in the central regions stayed dark.
This is due to the fact that some Africans were born with melanin deficiency making their skin white and more peachy looking. Because their skin was white and peachy looking, their skin couldn't take the sun giving them sun burns. so, they moved further out to a colder country.
Another answer:
The same reason he made all people. Skin color doesn't make any difference. It was out of love. And he wants us to love and worship him in return.
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It comes from a passage in the bible that could be interpreted as black people being cursed by god.
Some people believed god was punishing man for their sins, they began to wip and hurt themselves to try and make God forbive them of their sins. Like the albino character in the Davinci code.
They wiped themselves and tortured eachother.
Christians believed the black death was a punishment from god so the flagallant movement during the time of the black death was when people would offer bodily penance to god by whipping themselves in attempt to rid themselves of the black death.
Most of the people in the middle ages had faith in God. When the Black Death came, many lost faith because they thought God should have helped them and saved the faithful people from the Black Death.