The BJP is the main opposition to the federal ruling alliance led by the Congress party.
A team appointed by the supreme court to investigate several of the most deadly riots said that Kodnani and Jaideep Patel, a leader of the Vishwa Hindu Parishad party, led mobs that attacked Muslims in at least two areas where at least 106 people were killed.
"We are both innocent, we have been falsely charged in the case and we will prove it"
Vishwa Hindu Parishad leader
"The charges against Mayaben Kodnani includes abetment to murder, conspiracy to kill people and use of firearms," Mitesh Amin, Kodnani's lawyer, told reporters after her arrest.
If convicted she faces between seven years and life in jail.
Patel, who also was arrested, is expected to face similar charges.
They have both protested their innocence.
"We are both innocent, we have been falsely charged in the case and we will prove it," Patel said.
The religious violence was some of the worst since India's independence from Britain in 1947.
There have been sporadic bouts of violence between Hindus, who make up more than 80 per cent of India's population, and Muslims, who with 14 percent form the country's largest religious minority.