Guide to the Philippines conflict
The southern Philippines has a long history of conflict, with armed groups including Muslim separatists, communists, clan militias and criminal groups all active in the area.
Three groups comprise the Muslim separatists - the Moro National Liberation Front (MNLF), the Moro Islamic Liberation Front (MILF) and the Abu Sayyaf. The MILF and the Abu Sayyaf are breakaway factions of the MNLF.
The communist insurgency, on the other hand, is propagated by the Communist Party of the Philippines' (CPP) military wing, the New People's Army (NPA).
Most of the conflict in the south is in the remote islands of central Mindanao, especially on Basilan and Jolo.
BBC News looks at the main rebel groups.
Moro National Liberation Front
In Mindanao, the followers of Islam - referred to as Moros or Moors by the Spaniards during the colonial period - make up a sizeable part of the population.
Nur Misuari founded the Moro National Liberation Front (MNLF) in 1971, with the goal of fighting the Philippine state for an independent Moro nation.
An intervention by the UN-backed Organization of Islamic Conference - later called the Organization of Islamic Cooperation - led to the signing of the often-referred to Tripoli Agreement in Libya in 1976. This agreement, however, failed to hold.
In 1986, President Corazon Aquino personally met Misuari to hold talks. In 1989, Ms Aquino signed a law that gave predominantly Muslim areas in the region a degree of self-rule, setting up the Autonomous Region in Muslim Mindanao (ARMM).
The ARMM is composed of the mainland provinces of Maguindanao and Lanao del Sur, and the island provinces of Sulu, Tawi-Tawi and Basilan.
But the significant peace agreement with the MNLF was signed in 1996, with President Fidel Ramos. This paved the way for Misuari to run for office and he was elected as ARMM governor the same year.
His term however ended in violence in November 2001, when he led a failed uprising. He was subsequently jailed, but eventually released, in 2008.
In February 2005, supporters loyal to Misuari launched a series of attacks on army troops in Jolo, the largest of the Sulu islands.
The trigger for the violence was thought to be the launch of a huge military operation to target the armed Muslim group Abu Sayyaf - which is alleged to have ties with the Misuari faction.
In August 2007, the group said it was behind an ambush on troops in Jolo, which led to nearly 60 deaths.
In 2008, Misuari was ousted as MNLF chairman. Muslimim Sema succeeded him.
Over the years, the MNLF is believed to have become weaker, and many factions have splintered from the main group.
The Moro Islamic Liberation Front
The Moro Islamic Liberation Front is considered the country's largest Muslim rebel group. It was formed in 1981 after its leader, Salamat Hashim, split from the MNLF in 1978.
The MILF has had a long-term aim of creating a separate Islamic state in the southern Philippines.
Since 1997, the group has had a series of peace talks with the Philippine government, most of which were brokered by Malaysia from 2003 onwards.
In 2008, the government under President Gloria Arroyo said it had reached an agreement with the MILF on the boundaries for a Muslim homeland.
However the Philippine Supreme Court ruled that the draft agreement was unconstitutional and the failure of negotiations prompted renewed fighting.
President Benigno Aquino held talks with MILF leaders in Tokyo in 2011 to speed up the peace process.
On 7 October, he announced that the government had reached a framework peace agreement with the MILF after talks in Malaysia.
The agreement is expected to be formally signed on 15 October and a "comprehensive deal" reached by the end of the year.
The approval of the law will be through a plebiscite, with a final peace deal expected before Mr Aquino ends his presidency in 2016, officials say.
The agreement calls for the formation of a new, larger autonomous region in Mindanao to be named Bangsamoro after the Muslims living there.
Some key points include the gradual decommissioning of MILF forces, a guarantee of democratic and human rights, and the expansion of Sharia courts for Muslim residents.
The Abu Sayyaf
The Abu Sayyaf is the smallest and most radical of the Islamic separatist groups in the southern Philippines. They are known to carry out kidnappings for ransom and bombings to achieve their stated goal of an independent Islamic state in Mindanao and the Sulu islands.
The government views the rebels as little more than criminals and refuses to hold any form of talks with them.
Abu Sayyaf - which means "Bearer of the Sword" in Arabic - split from the MNLF in 1991 under the leadership of Abdurajik Abubakar Janjalani, who was killed in a clash with Philippine police in December 1998.
His younger brother, Khadafi Janjalani, followed as leader. He was also killed by Philippine troops in September 2006.
Reports in June 2007 said Abu Sayyaf had chosen Yasser Igasan, one of the group's founders, to succeed Janjalani as leader.
Both the MNLF and MILF have condemned the Abu Sayyaf's activities, and the US has included the group in its list of "terrorist" organisations, saying it has links with Osama Bin Laden's al-Qaeda network.
Nationwide support for the Abu Sayyaf is limited, but analysts say many locals in its stronghold areas of Jolo and Basilan tolerate the rebels and even work for them, attracted by the prospect of receiving lucrative ransom payments.
US troops have been helping the Philippine military fight the Abu Sayyaf, although they are limited to a training and advisory position because the Philippine Constitution bans foreign troops from taking part in actual combat.
In June 2002, US-trained Philippine commandos tried to rescue three hostages held on Basilan island. Two of the hostages - one an American citizen - were killed in the resulting shootout.
The group has also claimed responsibility for a series of bomb attacks over the years, including an attack on a passenger ferry in Manila Bay in February 2004 that killed 100 people.
From 2008 to 2011, the group conducted a series of kidnappings for ransom. Kidnap victims include a group of Filipino journalists in 2008; foreign members of the International Committee of the Red Cross in 2009; and two Filipino-Americans in 2011.
All of the victims have been released. In some cases, it was not clear whether ransom had been paid.
An Australian man, kidnapped in 2011, is currently still in captivity.
Since launching a major operation in August 2006 against the Abu Sayyaf, Manila has claimed a series of successes - including the deaths of Khadafi Janjalani and senior leaders Abu Sulaiman, also known as Jainal Antal Sali in 2007, and Albader Parad in 2010.
In December 2009, Philippine officials said that they had arrested an Abu Sayyaf founder - Abdul Basir Latip - who was allegedly been involved in kidnapping foreigners and Christians.
Abdul Basir Latip has also been accused of forging links between Abu Sayyaf and other militant Islamist groups, such as Jemaah Islamiah and al-Qaeda.
The New People's Army
The New People's Army (NPA) is the military wing of the Communist Party of the Philippines (CPP), which was established in 1969 by Jose Maria Sison.
The CPP - considered as one of the oldest communist insurgencies in the world - aims to overthrow the Philippine government using guerrilla-style warfare.
The insurgency waged by the NPA over the years is reported to be one of the deadliest in the Philippines, with local reports putting the number at least 40,000. The group is listed on the Foreign Terrorist Organisation list of the US State Department.
While the CPP was initially established with Maoist leanings and modelled after the agrarian revolution, the Communist Party of China had said in 2011 that they no longer support the CPP.
The CPP had its heyday in the 1980s during Martial Law, but its influence has since waned.
Analysts estimate that the NPA currently has at least 10,000 members. They have been credited with the kidnappings of locals and foreigners, extortion and killings.
Many of the NPA's senior figures - including founder Jose Maria Sison - live in self-imposed exile in the Netherlands and claim to direct operations from there.
Talks between the CPP's political arm and the government have been sporadic over the years.
In 2004, a peace process was revived, with representatives of the rebel group meeting government officials in the Norwegian capital of Oslo. But peace talks were suspended after rebels blamed the government for their inclusion in the US list of terrorist groups.
In August 2007, Sison was indicted in the Netherlands for ordering the murders of two former communist associates - Romulo Kintanar in 2003 and Arturo Tabara in 2004 - but the charges have since been dropped.
The Armed Forces of the Philippines in 2011 declared at least 23 provinces free from the NPA. The CPP refutes the claim.
The most recent high-profile formal talks between the government and the CPP were in Oslo in 2011. However, an agreement has yet to be reached.