The 70-year-old was also charged with war crimes and torture during his eight years in power in Chad, where rights groups say 40,000 people were killed under his rule, a court source and his lawyers told AFP.
Habre's legal team said genocide was among the main charges he faced and that he would be remanded in custody in Dakar.
Habre -- once dubbed "Africa's Pinochet" -- had been in a police cell in the Senegalese capital since his arrest on Sunday at the home he shares with his wife and children, according to a security source.
He added that prosecutors considered Habre to have "prime responsibility for the repression" carried out during his reign in Chad from 1982 to 1990.
Delayed for years by Senegal where he has lived since being ousted in 1990, Habre's trial will set a historic precedent as until now African leaders accused of atrocities have only been tried in international courts.
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