New People's Army (Communist rebels)
Moro National Liberation Front (MNLF)
Followers of Islam - called Moros or Moors by the Spanish - make up a sizeable population of the region.
The Moro National Liberation Front first appeared in the early 1970s, fighting for an independent Moro nation.
The group signed a peace agreement with the Manila Government in 1976, but this failed to stick.
Another agreement, signed in 1996, gave predominantly Muslim areas 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.
As part of the deal, the MNLF chairman and founder of the group, Nur Misuari, was installed as the new regional governor.
But his rule ended in violence in November 2001, when he led a failed uprising. He is now in jail.
Another MNLF leader, Parouk Hussin, took over as ARMM governor in 2002.
Parouk Hussin still retains a loyal support base, but the MNLF has become weaker over the years, and many factions have splintered from the main group.
Nur Misuari still has a small band of followers, who remain actively opposed to the current situation.
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.
There were no major skirmishes until August 2007, when the group said it was behind an ambush on troops in Jolo which led to some of the heaviest fighting in recent years, with nearly 60 dead.
MNLF said the ambush had been in retaliation for an army offensive a day earlier that killed four of its members, including a commander.
Click here to return
Moro Islamic Liberation Front (MILF)
The Moro Islamic Liberation Front is a more militant rebel group, which split from the MNLF in 1977.
The MILF has a long-term aim of creating a separate Islamic state in the southern Philippines, but analysts say the group may well settle for a certain degree of Muslim autonomy.
The MILF puts more emphasis on its Islamic roots than the MNLF. Many of its senior figures are clerics.
Based in central Mindanao, the MILF has broad popular support in rural areas, where the lack of economic development has encouraged dissent.
The 12,500-strong group was subject to a crackdown in 2000 under the army of then-president Joseph Estrada.
Rebels groups in Mindanao
MILF: 12,000 members, 9,000 firearms
CPP/NPA: 3,400 members, 2,300 firearms
Abu Sayyaf: 450 members, 350 firearms
Misuari followers: 450 members, 450 firearms
Pentagon group: 200 members, 40 firearms
Source: Army intelligence figures 2003
But the mood turned when Gloria Arroyo took power, after Mr Estrada was deposed amid popular protests in 2001.
Talks between Manila and the rebels were revived, although they stumbled to a halt a couple of years later when the group was accused of harbouring a gang accused of kidnapping foreigners.
MILF was also accused of being behind a bomb blast at Davao City airport in March 2003 which killed 21 people - and multiple murder charges were filed against the group's founder and then leader, Salamat Hashim.
But as 2003 wore on, there were signs of a breakthrough in relations between Manila and the MILF.
Shortly before his death from a heart attack in July 2003, Salamat Hashim issued a statement renouncing terrorism and underlining the MILF's commitment to achieving a peace settlement.
A ceasefire was agreed that year, and both sides have since been engaged in trying to negotiate a peace deal.
One factor which is complicating this process is the allegation that MILF has links with foreign terrorists - including Jemaah Islamiah, the South East Asian group blamed for the 2002 Bali bombings. The MILF denies the claims.
Despite the truce, skirmishes continue between troops and MILF militants.
In July 2007, MILF fighters were involved in clashes on Basilan island that left 14 Philippine troops dead, 10 of them reportedly beheaded.
MILF said the military had violated the ceasefire agreement by entering its territory without permission, but denied beheading the soldiers or kidnapping the Italian priest which the troops were searching for.
Click here to return
Abu Sayyaf is the smallest and most radical of the Islamic separatist groups in the southern Philippines.
It is best-known for a series of kidnappings of Western nationals and Filipinos, for which it has received several large ransom payments.
In June 2002, US-trained Philippine commandos tried to rescue three hostages being held on Basilan island. Two of the hostages - one an American citizen - were killed in the resulting shootout.
Gloria Arroyo restarted negotiations with the MILF
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.
Abu Sayyaf's stated goal is an independent Islamic state in Mindanao and the Sulu islands, but the government views the rebels as little more than criminals, and refuses to hold any form of talks with them.
Abu Sayyaf - which means "Sword of God" 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, took over as leader, although he was killed by Philippines troops in September 2006.
Nationwide support for 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.
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.
US troops have been helping the Philippines military fight Abu Sayyaf, although they are limited to a training and advisory position as the Philippine constitution bans foreign troops from taking part in actual combat.
Since launching a major operation in August 2006, Manila has claimed a series of successes - including the deaths of Janjalani and another senior Abu Sayyaf leader, Abu Sulaiman, also known as Jainal Antal Sali, in January 2007.
Reports in June 2007 said Abu Sayyaf had chosen Yasser Igasan, one of the group's founders, to succeed Janjalani as leader.
But military chiefs believe Abu Sayyaf's numbers have now fallen to around 200, and they talk confidently of one day wiping out the rebel group entirely.
Click here to return
New People's Army (NPA)
The New People's Army is the military wing of the Communist Party of the Philippines (CPP), and has been in existence for more than 30 years.
The group, based on the island of Mindanao, has an estimated 10,000 members according to a presidential adviser on the peace process.
Peace talks between the CPP and the Philippine Government stalled in June 2001, after the NPA admitted killing a Filipino congressman.
Government troops have been told to hunt down the Abu Sayyaf
The CPP/NPA was added to Washington's list of foreign "terrorist" organisations in August 2002.
Shortly afterwards, at a request from the Americans, the Dutch Government cancelled benefit payments to group members living in the Netherlands.
Many of the NPA's senior figures, including its founder Jose Maria Sison, live in self-imposed exile in the Netherlands, and direct operations from there.
Unlike the Americans, the Philippine Government does not class the Maoist group as a terrorism organisation.
In February 2004 a peace process was revived, with representatives of the NPA meeting government officials in the Norwegian capital Oslo.
The two sides agreed a series of measures to move towards a formal peace deal.
These included setting up a joint commission to examine human rights abuses on both sides, and working together for the removal of the NPA from the US and EU's list of terrorist organisations.
Click here to return