The protesters marched to a mosque where unidentified men opened fire on a crowd and injured 10 men last week.
Cocoy Tulawie, a local official leading the protest, said the humanitarian mission by American troops was a cover for counterinsurgency operations and amounted to US intervention in domestic affairs.
"We should not allow their presence here," Tulawie told the crowd of protesters in front of a police station. "They’re meddling in our government’s affairs."
The protesters burned a mock US flag amid shouts of "Allahu Akbar (God is great)!" and raised anti-US placards. One read:
"Bud Daho, never again," referring to a Jolo area where American forces bloodily crushed a Muslim uprising about a century ago.
Policemen and a jeepload of Marines kept watch from a distance.
American forces do not take part in counterinsurgency operations and focus on humanitarian projects, US and Philippine officials say.
American troops have arrived on the island in recent weeks to deliver dental care to residents, perform road repairs and distribute books under a counterterrorism program called "Bayanihan." Some were seen in action last week in a firing range in Patikul town using targets with the images of Osama bin Laden and Saddam Hussein as targets.
At least 250 US soldiers will arrive later this month for separate annual joint military exercises called "Balikatan," which will also focus delivery of medical and engineering services.
Security is a key concern during the US exercises because of the presence of al-Qaeda-linked Abu Sayyaf militants and a surfeit of unlicensed firearms in Jolo.
The Abu Sayyaf, which is on a US list of terrorist organizations, has been blamed for deadly bombings and high-profile ransom kidnappings, including of Americans. — AP