Seamus Daly, 43, from Cullaville, County Monaghan in the Irish Republic, has previously been found liable for the August 1998 Real IRA attack in County Tyrone in a landmark civil case.
He was last night charged with 29 counts of murder, two charges linked to the explosion in Omagh and two counts linked to an attempted explosion in Lisburn in April 1998.
Mr Daly was arrested by officers from the Police Service of Northern Ireland's Serious Crime Branch in the Newry area on Monday.
The 29 victims, who included a woman pregnant with twins, died when the dissident republican car bomb detonated in Omagh town centre on a busy Saturday afternoon.
Five years ago Mr Daly was one of four men found responsible for the bomb at Belfast High Court after being sued by some of the victims' families.
He is due to appear in court in Dungannon today.