On Nov. 16, the Philippine military declared Marawi city free of ISIS-inspired Maute group militants following the deaths of militant leaders Isnilon Hapilon and Omar Maute. The protracted five-month siege resulted in the deaths of 165 Filipino soldiers, 47 civilians and at least 900 militants and the reduction of the city to rubble. After its decimation in Marawi, the Maute group now virtually ceases to exist.

Duterte and his top military leaders have looked to seize the moment and take on the plethora of more well-established militant groups that operate on the Philippines’ restive southern island of Mindanao. After achieving victory over the Mautes, the president has placed the ISIS-inspired Bangsamoro Islamic Freedom Fighters (BIFF), the criminally-minded Islamist militants of Abu Sayyaf, and the Maoist rebels of the New People’s Army (NPA) firmly in his crosshairs. Yet given Mindanao’s long history of militancy, defeating this multitude of threats will prove a far harder task.

Despite the difficulties laying ahead, Duterte has been bullish when it comes to addressing security concerns in Mindanao. Shortly after installing Lieut. Gen. Leonardo Guerrero as the armed forces chief in late October, Duterte ordered him to create 10 new battalions and hire 13,000 new recruits to crush the remnants of ISIS and take on Maoist rebels.

Duterte’s top military leaders have displayed confidence in equal measure. Defence Secretary Delfin Lorenzana has vowed to redeploy units from Marawi to intensify operations against the NPA, while retiring armed forces chief Gen. Eduardo Ano has said ‘‘there will be no letup’’ in confronting Islamist militants, adding ‘‘It’s about time to end these terrorists here in Mindanao’’.

The most immediate threat emanates from the remaining radical jihadist elements, particularly the Bangsamoro Islamic Freedom Fighters, who pledged allegiance to ISIS along with Hapilon’s faction of Abu Sayyaf in 2014. The BIFF have separated into at least three distinct factions, the largest of which is led by Ismael Abubakar and remains active in North Cotabato and Maguindanao.

Since mid-November the military has conducted airstrikes in an attempt to dislodge BIFF in these provinces, yet the splintered nature of the group has hampered progress. In recent weeks, troops have reported seeing foreign-looking fighters within BIFF’s ranks, raising concerns that international jihadists may still be present in the southern Philippines.

Militants allied to Abu Sayyaf also remain active across the maritime provinces of Basilan, Sulu and Tawi-Tawi. Although Hapilon’s faction was wiped-out in Marawi, several other factions continue to pose a threat. The largest of these is located in Sulu, and is led by senior militant leader Radullan Sahiron. In Basilan, Furuji Indama is thought to lead a powerful sub-group. These factions continued to launch attacks in their strongholds throughout the Marawi crisis, indicating that the group retains several-hundred fighters.

In recent months Abu Sayyaf has rampaged through small towns killing civilians, has taken several groups of fishermen hostage in the Sulu Sea and clashed with the military on a regular basis – most recently on Nov 8 when the jihadists killed six Philippine soldiers.

Aside from the radical militants of BIFF and Abu Sayyaf, Duterte must also keep an eye on two larger – yet more moderate – Islamist groups based in Mindanao. The Moro National Liberation Front (MNLF) and Moro Islamic Liberation Front (MILF) have fought for greater autonomy for Mindanao’s Moro Muslim-minority population since the 1970s. Whilst both groups waged bloody guerrilla campaigns in the past, in recent years both the MILF and MNLF have laid down their arms in pursuit of a political settlement.

This process is not yet complete, as the proposed Bangsamoro Basic Law (BBL), which aims to resolve grievances by creating a new autonomous region in the south, is still being debated in Congress. Fears have been voiced that if the passage of the bill is delayed, the Moro separatist groups could return to violence.

Last month, Duterte warned that a failure of the peace process would leave Mindanao ‘‘headed for trouble’’. The MILF’s leader Al Haj Murad Ebrahim has echoed these fears, warning that ‘‘the longer this peace process takes, the more people are going to be radicalized,’’ playing straight into the hands of groups such as ISIS.

Peace talks with communist rebels have also stalled. Negotiations initiated by Duterte last year started off on a positive note and resulted in the declaration of a ceasefire, which initially held. However, talks reached deadlock and the ceasefire fell apart in early February, after Duterte’s refusal to release political prisoners led to a spate of rebel attacks. Several attempts have been made to restart negotiations; but all have failed. The situation has deteriorated to such an extent that Maoist attacks against police and military targets are occurring on an almost daily basis.

In Mindanao, the Philippine military is fighting on several fronts. It may have been able to defeat Maute in the confined urban setting of Marawi, but its resources are thinly stretched when having to operate across Mindanao and its outlying islands. Whereas Maute was a relatively newly-established group with a limited local support structure, the MILF, MNLF and the New People’s Army (NPA) are more resilient, having been around a lot longer.

The Moro separatist groups have fought for greater autonomy in the south since the 1970s, while the Maoists have waged a “protracted people’s war” across the country since 1969. Despite Duterte’s promises, inflicting a conventional military defeat on a well-established group such as the NPA will be extremely difficult – if not impossible.

Securing lasting peace agreements with large groupings such as the MILF and NPA will be key to scaling down Mindanao’s multiple armed insurgencies in the long-term. If the communist insurgency and Moro separatist struggle could indeed both by resolved through political channels, only the smaller, more radical Islamist groups – such as BIFF, Abu Sayyaf and any potential future ISIS-linked offshoots – would be left to tackle via military means.

As well as vowing to crush Mindanao’s various armed groups in the post-Marawi era, shifting the focus more toward reviving slow-burning peace processes would surely add weight to Duterte’s strategy for ending Mindanao’s militant scourge.

Michael Hart has researched for Action on Armed Violence (AOAV) and the International Institute for Strategic Studies (IISS). He blogs at https://asiaconflictwatch.com/