Abu Sayyaf chief Khadafy Janjalani and six members of his group have been charged for the murder of six people in the three bombing incidents.
The bombings occurred in Manila's Makati City and southern Philippines' Davao and General Santos cities on February 14.
Janjalani, together with Jainal Salt, also known as Abu Sulaiman, an Abu Sayyaf commander, and Jacky Zacky, were charged in absentia, State Prosecutor Emmanuel Velasco told Gulf News.
"They have to face these cases once they are arrested," said Velasco. He added that Janjalani's involvement in the Valentine's Day bombings came during interrogation of his co-accused.
Janjalani and the others were charged with multiple murders, frustrated murder and illegal possession of firearms before a regional trial court in Makati City, where six victims died and more than 100 others were wounded when a bomb exploded in a passenger bus. Two others died in the bombings in General Santos and Davao cities.
After the bombing incidents, Janjalani called up a radio station saying that the Abu Sayyaf group was responsible for the carnage.
Another accused, Solaiman, said the bomb attacks were in retaliation for the anti-insurgency campaign in Mindanao.
Zacky is not a well-known Abu Sayyaf leader, but he was among the six who were recently charged. Gamal Baharan, known as Tapay, was charged with illegal procurement of firearms and explosives.
Also accused was Angelo Trinidad, 26, known as Abu Khalil and another Abu Sayyaf activist Maidan.
Baharan and Trinidad were arrested on February 21. They admitted their alleged role in the Makati bombing, adding that they were bothered by their conscience that was why they identified the others who were involved in the February 14 bombings.
Baharan and Trinidad boarded the ill-fated vehicle and hurriedly alighted from it a few minutes before the explosives they planted went off, a witness has said. Also accused was Ganal Bannah, known as Boy Negro, who admitted that he supplied the explosives to Baharan. He was arrested on March 4.
"The evidences against Baharan, Trinidad, and Bannah were their voluntary confessions and the statements they gave to the media," said Velasco. The three are currently detained at the police headquarters in Camp Aguinaldo in suburban Quezon City.