MANILA -- In August 2011, President Benigno S. Aquino III flew secretly to Tokyo to meet with the leader of the Philippines' largest Muslim separatist group. The meeting, with the chairman of the Moro Islamic Liberation Front, Al Haj Murad Ebrahim, led to a landmark October 2012 framework agreement for peace.
But in the year since, Mr. Aquino has received a rough reminder that the quest for peace in the southern Philippine island of Mindanao, one that goes back more than a century, remains as difficult as ever.
The most recent fighting, in Zamboanga, began last Monday when several hundred armed members of the Moro National Liberation Front, a rebel group that was not included in the 2012 peace deal, entered the port city by sea and, the police said, declared an independent Islamic state.
Under attack by police and the army, the rebels took hostages and retreated to the poor Muslim areas outside the city, where on Sunday they were fighting house to house with the security forces. Officials said that nearly 100 rebels had been killed or captured, and that many had cast off their military fatigues in an effort to blend into the civilian population.
Over all, more than 50 people have been killed, and nearly 70,000 displaced, in the battles during the past week between the military and the rebels, officials said.
The latest fighting is not the first major challenge to the 2012 peace deal. In February, more than 100 armed men traveled by boat from the southern Philippines to the nearby Malaysian state of Sabah, on the island of Borneo, and claimed the area for descendants of the Sultanate of Sulu, which controlled the area in the 1800s. The incursion killed more than 60 people, escalated into the most serious security threat in Malaysia in more than a decade and strained relations with the Philippines.
In addition to these high-profile episodes, Mindanao faces grinding, almost daily violence, including kidnappings, banditry, summary executions and roadside bombs.
Between June 1 and Aug. 15, there were 61 incidents in Mindanao related to Muslim insurgency groups, according to a report by Pacific Strategies and Assessments, a risk-mitigation firm in Manila. That was double the average since August 2009, the report said.
They included a bombing that killed nine people and wounded at least 50 in the city of Cagayan de Oro on July 26 and a roadside bomb that killed eight and injured 30 near Cotabato City on Aug. 5.
At the root of the problem is a belief by many Muslims in the southern part of the country that Christians in the north have oppressed them and exploited their resources. Well-armed Muslim clans have fought government forces since the American military quelled the Moro insurrectionists in 1899, when the Philippines was under colonial rule by the United States. Every government in Manila since independence in 1946 has struggled to bring peace to Mindanao.
Any peace deal is complicated by factionalism, with ancient roots, among the political and rebel organizations involved, said Ramon C. Casiple, executive director of the Institute for Political and Electoral Reform in Manila.
"The power structure of the clans and tribes transcends the power of the political groups," Mr. Casiple said. "Whatever group they are aligned with, their allegiance is to their clan."
As a result, the Manila government must deal with a complex web of myriad groups -- either through negotiations or the use of force -- that have repeatedly changed alliances based on clan loyalties or charismatic leaders.
The Moro Islamic Liberation Front, which signed last year's deal, was originally a splinter group of the Moro National Liberation Front, a faction of which is now fighting in Zamboanga.
Fighting that broke out last week on the nearby island of Basilan was touched off by two other splinter groups: Abu Sayyaf, which has been linked to Al Qaeda, and the Bangsamoro Islamic Freedom Fighters. The police suspect another breakaway group, the Khilafah Islamiyah Movement, in the July and August bombings. A splinter group of the Sultunate of Sulu launched the February incursion into Malaysia.
The government sought to bring other groups into the talks that led to the peace deal with the Moro Islamic Liberation Front. The goal, peace negotiators said, was to forge an umbrella agreement that would create a lasting peace.
That clearly has not happened. The group fighting in Zamboanga has said part of its motivation was opposition to the 2012 deal, which its leaders feel undercut a previous agreement with the government.
The current fighting is not likely to derail the peace deal, said Richard C. Jacobson, the Philippines country director for Pacific Strategies and Assessments, but it will make it harder to put the power-sharing part of the agreement into effect.
As part of that deal, the Moro Islamic Liberation Front is to have greater autonomy to handle security in the areas where it operates. This will include dealing with rival groups and with organizations committed to armed struggle for an independent Islamic state in Mindanao.
"When they are in power, how will the Moro Islamic Liberation Front handle a situation like we are seeing now in Zamboanga City?" Mr. Jacobson asked.
The peace deal also includes a wealth-sharing agreement stipulating that 75 percent of the tax revenue from metallic minerals mined in the region will stay in Mindanao. In addition, 50 percent of the taxes collected from fossil fuels developed in the region will remain.
How this influx of revenue is managed is a key consideration for peace in the region, Mr. Jacobson said. He said that the region had weak government institutions in areas like law enforcement, education and health care, and that corruption was a profound problem.
"If people in these areas don't see improvements, if they don't see results, it gives the armed groups the motivation and opportunity to fill that gap," Mr. Jacobson said.
Mr. Casiple said that even if the peace agreement was successfully put into practice, security would continue to be challenged by the thousands of unregistered weapons that were acquired in decades of insurgency in the region.
This article originally appeared in The New York Times.