The Iraqi suspects, identified only as Twana H. S. and Asia R. A. , are accused of genocide, crimes against humanity, war crimes and membership of a foreign terrorist organisation, the federal prosecutor's office said.
They were arrested Tuesday in Regensburg and the Roth district, both in the southern state of Bavaria.
The pair were married under Islamic law and were members of IS in Iraq and Syria from 2015 to 2017. During this time they held two Yazidi girls, aged five and 12, as slaves, according to prosecutors.
The Yazidis are a Kurdish-speaking group hailing from northern Iraq. They have for years been persecuted by IS militants who have killed hundreds of men, raped women and forcibly recruited children as fighters.
Twana H. S. repeatedly raped both children, with the help of Asia R. A. , who prepared a room and put make-up on one of the girls, they said.
The girls were punished with "harsh physical violence" when they made what the suspects viewed as mistakes. The elder girl was beaten with a broomstick while the younger one's hand was scalded with hot water, the prosecutors said.
The suspects are accused of exploiting the children by forcing them to do housework.
They also allegedly stopped them from practising their own religion, forcing them instead to follow Islam.
Before leaving Syria in November, 2017, the suspects handed the girls over to other members of IS, the prosecutors said.
"All of this served the organisation's objective to destroy the Yazidi religion," they said in a statement.
The suspects are being held in pre-trial detention.
In another case, a German woman who joined the jihadist group was last year handed a 14-year jail term by a Munich court for enslaving a five-year-old Yazidi girl and letting her die of thirst.
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