The 66-year-old listened on Thursday as prosecutor Salman Maryadi also re-accused him of leading the outlawed Islamist group Jemaah Islamiya (JI), despite having been found not guilty of the same charge earlier in 2004.
Nevertheless, prosecutors told the heavily-guarded courtroom in south Jakarta that the defendant sought to establish an Islamic state in Southeast Asia by violent means.
Bashir could face a death sentence if found guilty under tough new anti-terrorism laws. Maryadi told judges that Bashir incited others to carry out last year's Jakarta Marriott hotel bombing which killed 12 people.
In a second count to be heard at his trial, he faces a possible 20 years to life in prison under the criminal code for involvement in "a sinister conspiracy" which endangers or takes the lives of others.
The charge relates to the bombing on the resort island of Bali, which killed 202 people on 12 October 2002.
The preacher declared his innocence after arriving at the court flanked by heavily armed anti-terrorism police. Around 650 police, including snipers, ringed the court building.
"It is clear that I feel I am innocent ... all who do not agree with George Bush's interests are terrorists," he said.
Bashir and his lawyers have repeatedly said his detention and trials are the result of pressure from the US.
His conviction and sentence of four years in jail in September 2003 for involvement in a JI plot to overthrow the government was quashed by higher courts.
Judges said then there was no proof he led any Islamist network.
Amid strong protest by his supporters, Bashir was re-arrested by police on suspicion of terrorism last April moments after he finished serving a 18-month jail term for immigration offences.