The victims were based in Florida and Puerto Rico, the military said.
Police in this U.S. Caribbean territory said they had recovered seven bodies, some charred and dismembered, in addition to parts of the fuselage.
The bulky MC-130H struck a heavily wooded area on the outskirts of the town of Caguas, 20 miles south of San Juan, while flying in rain and fog during a training mission Wednesday night.
It was the second accident in as many months involving a Combat Talon II, a special operations variant of the C-130 Hercules cargo plane. The other crashed in June while taking off from an airstrip in Afghanistan, killing three U.S. military personnel.
People who saw Wednesday's crash told reporters the low-flying plane plowed through trees, smashed into Mount Perucho, broke in two and erupted in flames, scattering body parts and bits of plane.
Eulalia Martinez said the impact made her house tremble and flames lit up the night sky. "Everything was very bright, very bright, and with the force the house shook," the 75-year-old woman said on WAPA Radio.
Rescuers carrying stretchers and supplies climbed a narrow mountain trail made treacherous by rain, fog, dense woods and soggy underbrush. Using ropes, they rappelled down an 80-foot drop to recover one body.
As the fog lifted Thursday afternoon, two forensic dogs arrived to join the search, panting from the a 1 1/2-hour hike.
Three helicopters circled the crash site but were forced by clouds to retreat at least once and land at a baseball park being used as a base for the recovery work.
Rescuers carried the bodies, on stretchers covered with white plastic, to the ball park, from where they were to be flown by helicopter to Roosevelt Roads Naval Station, according to Rafael Guzman, executive director of the State Emergency Management Agency.
He said the search was called off at sunset but would resume at first light Friday. "We believe that the three missing bodies are those of the pilot, co-pilot and engineer, which would have been in the cockpit" which took the brunt of the impact, Guzman told The Associated Press.
"Military officials on the scene have confirmed there are no survivors," Steve Lucas, a spokesman for the United States Southern Command in Miami, told the AP.
He said seven crew members aboard the aircraft were based at Hurlburt Field, near Fort Walton Beach in Florida, and the three others were from Puerto Rico. The names of the victims would be withheld until relatives were informed, Lucas said.
However, an official in Louisville said two Kentucky Air National Guard members were on the flight manifest. Lt. Col. Phil Miller said the family had been informed that they were scheduled to be on the flight.
The plane belonged to the Air Force Special Operations Command and was on a training mission from Roosevelt Roads Naval Station in northern Puerto Rico to the Borinquen Air Station on the west coast of the island.
The plane that crashed in Afghanistan, which also was from Hurlburt Field, is being investigated by two separate boards. Officials said it was unlikely the $155 million, four-engine turboprop was shot down.