"His motives were largely political," Mr Moreno-Ocampo said.
"His alibi was a 'counterinsurgency'. His intent was genocide."
Pro-government militias allegedly followed Mr Bashir's orders to attack and destroy villages from the three groups, pursuing survivors into the desert.
Those who reached camps for displaced people faced further violence, Mr Moreno-Ocampo alleged:
"In the camps Bashir's forces kill the men and rape the women. I don't have the luxury to look away. I have evidence."
Mr Moreno-Ocampo accused the Sudanese president of using his "absolute control" of the state apparatus to conceal the truth and protect his subordinates "in order to secure their willingness to commit genocide".
The UN has already raised the security alert level for its staff in Darfur. The joint United Nations-African Union Mission in Darfur (Unamid), which has 9,000 troops, has been struggling to contain the violence.
The ICC was set up in 2002 as the world's first permanent war crimes court.
Other international courts have previously indicted Serbia's President Slobodan Milosevic and President Charles Taylor of Liberia.
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