The southern Philippines is home to lush virgin forest, untapped natural resources and some of the most violent armed groups in Southeast Asia -- including the al-Qaida linked Jemaah Islamiyah, or J.I. The Philippine government is in its second month of a new major offensive against J.I.-affiliated armed groups in the country's south.

Deep in the thick jungle and mountains on the Philippines' second largest island, Mindanao, Jemaah Islamiyah thrived -- setting up training camps that produced thousands of Muslim militants from the late 1990s until 2003.

J.I. is blamed for a series of deadly bombings in the Philippines and Indonesia, which have killed hundreds of people over the past few years.

The group, which is linked to the al-Qaida terror network, aims to establish an Islamic state across much of Southeast Asia -- including Indonesia, Malaysia, and the Muslim parts of Thailand and the southern Philippines.

Jemaah Islamiyah Training Camps

The Philippine government closed many of the J.I. training camps during a major offensive in 2003. However, National Security Advisor Norberto Gonzales cautions more are cropping up.

"We launched some operations in Sulu and out there during the operations we have uncovered their training ground and their place for manufacturing the explosives," says Gonzales.

Mindanao and the nearby islands of Sulu and Basilan have been the battlegrounds for several Muslim separatist groups for more than three decades.

The Moro Islamic Liberation Front

One of those groups is the Moro National Liberation Front. It signed a peace pact with the government a decade ago. The splinter Moro Islamic Liberation Front, or M.I.L.F., also signed a ceasefire with Manila in 2003 and is now negotiating a final peace deal.

The most violent group is the Abu Sayyaf. The gang once known for its kidnap-for-ransom tactics abducted hundreds of people, including foreign tourists. National Security Advisor Gonzales says it appears to have now embraced jihad, or holy war.

"We launched a major offensive on the Abu Sayyaf . . . [who] have decided to become religious or ideological in character. Since then they have really minimized their kidnapping efforts and concentrated more on terrorist acts. And we know for a fact that Abu Sayyaf is the only organization that has official links with J.I," says Gonzales.

The authorities believe two of J.I.'s most wanted members are hiding in Sulu. Indonesians Dulmatin and Umar Patek have been linked to the 2002 bombing at Bali, Indonesia that killed 202 people.

Filipino soldiers escort Hilarion Del Rosario Santos, center, leader of a radical Islamic group

The United States has been helping the Philippines in the war against terrorism since 2002. It has offered millions of dollars for the capture of Dulmatin and Umar Patek. They and the leaders of the Abu Sayyaf are now the subjects of a military manhunt here in the south.

The extent of J.I.'s reach into the Philippines became even more evident after the 2003 arrest of 33-year-old Indonesian, Taufik Rifki, who admitted to police he was J.I.'s finance officer here.

Speaking from a jail in South Cotabato, where he is awaiting trial for a series of bombings in Mindanao, Rifki now denies he was ever a member of J.I.

He says he came to the Philippines around 2000 as a small businessman looking for adventure and new experiences. But he says his Islamic faith give him solace in his predicament. While armed Islamic separatist groups in the south of the overwhelmingly Catholic Philippines have long been a problem, it is only in the past few years that they have joined forces with Jemaah Islamiyah.

The Moro Islamic Liberation Front is based on Mindanao. It once sheltered the J.I. main camp, Abubakar, where it trained recruits and ran the isolated area like a mini-city that included a jail, field hospital and mosque.

The Philippine military captured the camp in 2003 and now uses it as a base. But the base's Lieutenant Colonel Roland Heuqueriza says J.I. still has small training camps, which are more difficult to find than was Abubakar. "It is really hard because we tried our best to penetrate the area. But it's really hard to penetrate because of the terrain, thick forest, and still virgin forest," says Heuqueriza.

M.I.L.F. spokesman, Eid Kabalu, denies any ties between his group and J.I. "The M.I.L.F. is a legitimate organization pursuing a legitimate cause and we don't need to ally ourselves with a terrorist organization just to pursue our cause," says Kabalu.

While the Philippine government confirms the M.I.L.F. has broken ties with J.I., Manila remains concerned about splinter groups both inside and outside the organization. 

Links with Indonesia?

Philippines rebel Abu Sabaya

National Security Advisor Gonzales says J.I. radicals from Indonesia are preaching a more fundamentalist Islam. He says it appeals to disaffected young Muslim men in the south who are forming new cells at small camps.

"We continue to assume that the traffic between Indonesia and the Philippines continues in terms of terrorist operatives. And that, yes, some form of training is continuing in Mindanao. The major camps that they were talking about were dismantled. It doesn't mean that there are no new camps. So this is continuing," says Gonzales.

And Gonzales fears the southern region's lawlessness, underdevelopment and proliferation of arms, makes it a powder keg waiting to explode. "It's a matter of time. If the ideological discussion matures, then all groups, all religious groups in the region inclined to terrorism will start pouring their resources to the Philippines because we have the armies."

And while people here continue to eke out a living from the land, mired in poverty and lacking even the basic infrastructure, it is likely the volatile region of the southern Philippines will continue to be a magnet for Muslim radicals looking for a haven.

This story was first broadcast on the English news program,VOA News Now. For other Focus reports click here.