Rolando del Torchio, 56, was the fourth foreigner kidnapped in the region in three weeks, and brings to eight the number believed to be held by the Abu Sayyaf group, listed by the United States as a terrorist organisation.
The kidnappings show the Abu Sayyaf is regaining strength in the south, a desperately poor region home to most of the nation's Muslim minority, after a US-backed military campaign was scaled down this year, analysts said.
"This shows that the Abu Sayyaf is not only regaining its old shape and form, it is also reaching a new level of sophistication," Rodolfo Mendoza, a senior analyst at the Philippine Institute for Peace Violence and Terrorism Research, told AFP.
During its heyday in the 2000s, the Abu Sayyaf ransomed off dozens of foreigners from raids as far off as Malaysia's Sipadan island, until its key leaders died in military assaults aided by the United States.
Mendoza noted how in the most recent kidnappings, the Abu Sayyaf struck on opposite ends of the main southern island of Mindanao, an unusually wide arc for their raids for recent years.
On Wednesday night, six suspects seized Del Torchio from a pizza shop he ran in the sleepy port city of Dipolog, then fled by speedboat towards Jolo, the Abu Sayyaf's island stronghold on the country's southwestern tip.
Dipolog is about 400 kilometres (240 miles) from Jolo, a small island where the militants enjoy support of local communities and have the upper hand against the military in remote jungle and mountainous terrain.
Three weeks ago, gunmen seized two Canadians, a Norwegian and a Filipina from the resort island of Samal, about 500 kilometres from Jolo.
Mendoza said the group was brought to Jolo, although the military has not verified this.
Abu Sayyaf thriving
Mendoza said a stronger US military presence could have helped the Philippines track the Abu Sayyaf, which is only believed to have a few hundred gunmen but easily replenishes its numbers from local communities.
The United States had between 500-600 special forces stationed in the south to train local forces from early 2002, but withdrew most of them last year.
"The US has the capacity to help manage this situation. They have drones, we don't," he said.
Aside from kidnappings, the Abu Sayyaf, has also been blamed for the country's worst terrorist attacks including the 2004 bombing of a Manila ferry that killed over 100 people.
Analysts said the kidnapping spree could also have been aided by corrupt politicians, who fund their campaigns with ransom money.
Marc Singer, director for business intelligence at Pacific Strategies and Assessments in Manila, noted a trend of rising kidnappings in the Philippines during election season.
"They (Abu Sayyaf) do work hand in hand with corrupt local officials and as election time nears there is a need to raise revenues," Singer told AFP.
The Philippines will hold general elections in May next year.
Last year, the Abu Sayyaf claimed it got $5.4 million in exchange for two German hostages it had held in the jungles of Jolo for six months.
"This emboldened the Abu Sayyaf for subsequent kidnappings. It definitely is profitable for them," Singer said.
Abu Sayyaf last year pledged allegiance over the Internet to the Islamic State group, though many analysts believe the group has little ideology other than to win ransom paydays via kidnappings.
The Abu Sayyaf is holding a Dutch man, a Korean and two Malaysians in the Jolo jungles, according to the military.
In August, it beheaded a local village official on Jolo after the government refused to pay a ransom.
The latest kidnap victim, Del Torchio, worked as a missionary for the international organisation PIME in the south from 1998 before retiring in 2000, colleagues said.
"He was a jolly, good fellow, always full of energy, full of ideas, always trying to do something different," PIME Philippines head Gianni Re told AFP.
Three of the group's members have been kidnapped in the past but were eventually released.