Juromee Dongon was married to a senior leader of the notorious Abu Sayyaf kidnap-for-ransom group, Khadaffy Janjalani. After his death in 2006 she married Malaysian bombmaker Zulkifli bin Hir, alias Marwan, who was killed in 2015 in the Philippines, police said.
Authorities arrested Dongon along with her relatives in her home in Lanao del Norte province in the restive southern region of Mindanao where they found firearms, ammunition and bomb-making components, a police statement said.
"She assists, associates, networks and supports terrorist groups," regional police spokesman Superintendent Lemuel Gonda told AFP.
Marwan was a leading member of Jemaah Islamiyah (JI) and a suspect in the 2002 Bali nightclub bombings that killed 202 people as well as in two deadly Philippine attacks.
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He died in a raid in the southern Philippines that also left 44 police commandos dead. The US had offered a $5 million bounty for him.
In two operations on Sunday, police arrested Dongon as well as her two sisters and father, Gonda said, adding the family had "connections with terrorists".
Abu Sayyaf is an Islamist militant group which was set up in the 1990s with seed money from the Al-Qaeda network, and has been blamed for the worst terror attacks in the Philippines' history, including bombings.
The Abu Sayyaf had harboured JI militants in their bases in remote southern islands, including key suspects in the Bali bombings.
Security analysts have said widows of militant leaders played important roles in extremist groups as they enhanced the status of their second husbands.