Bashir was cleared last year of charges that he headed Jemaah Islamiyah, the al-Qaida- linked terror group blamed for the two bombings.
This time, prosecutors will attempt to prove Bashir incited his followers to attack the Marriott hotel, killing 12, and that he authorized the Bali operation, in which 202 people, most of them foreign tourists, perished.
If found guilty of the first charge, he could face the death penalty.
Bashir, 66, has consistently denied any wrongdoing, and claims that Jemaah Islamiyah does not exist.
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