First, a motorcycle bomb exploded on a southern island where al Qaeda-linked militants are active, killing at least two and wounding two dozen. Hours later, a car bomb in predominantly Christian Iligan city wounded at least 11, including two soldiers, police said.
No group has claimed responsibility for either one.
The motorcycle in downtown Jolo was parked across from a store that was wrecked in the early morning blast, killing the store owner instantly, police and the military said.
At least two were confirmed dead, but the number of fatalities was expected to rise because many of the wounded - including two policemen - were in critical condition, said regional military commander Maj. Gen. Juancho Sabban.
Most of the wounded were students on their way to school, and authorities suspended classes in Jolo for fear of more attacks.
Sabban said a bomb squad was defusing a roadside explosive discovered close to the Jolo Roman Catholic cathedral when the motorcycle bomb went off nearby.
Jolo Mayor Hussin Amin said the motorcycle was left unattended for a few hours, arousing suspicion. The bomb exploded just as three officers were approaching the vehicle, wounding them.
Sabban blamed the bombing on Abu Sayyaf militants, the target of a major military operation after they kidnapped three Red Cross workers in January. The militants are still holding one ailing hostage, Italian Eugenio Vagni, while the others have been freed.
Sabban said the blast may be a diversionary tactic to relieve the pressure on the gunmen holding the Italian.
The car bomb in Iligan city, on the main southern island of Mindanao, was detonated by cell phone moments after a military jeep pulled next to the vehicle, said police chief Leonardo Esclamado. At least nine civilians were among the wounded, he said.
He said a bomb squad was sifting through the wrecked car to determine the type of explosives used.
The two blasts follow Sunday's explosion outside a Catholic cathedral in Cotabato city, about 56 miles (90 kilometers) from Iligan, which killed six people and wounded scores others in an attack the military blamed on the separatist Moro Islamic Liberation Front.
The rebels denied it. They have waged a decades-long battle for self-rule in the southern Mindanao region, homeland of Muslims in this predominantly Roman Catholic nation.
Malaysian-brokered peace talks between the government and the rebels collapsed last year when a preliminary deal on an expanded Muslim autonomous region fell apart, sparking deadly clashes that have displaced large numbers of villagers.
Sabban said the Jolo and Cotabato blasts appeared to be unrelated but had the same effect: sowing terror and panic.
Unlike the Moro rebels, who are pursuing on-and-off talks with the government, the Abu Sayyaf is considered a terrorist organization because of its al Qaeda links and many terrorist attacks, including ones on Americans.
The group and its allies, numbering about 400, have turned to kidnappings to make money in recent years, raising concerns among Philippine and U.S. security officials that ransom payments could revive the group, which has been weakened by years of U.S.-backed offensives.