The discovery was made at the El Rancho Restaurante, located in the 200 block of Fulton Street in the Chambersburg section of the city.
The building's fire alarm was pulled, triggering a response from firefighters who found the bodies in the basement of the restaurant.
The two victims had apparent gunshot wounds.
"We're still piecing things together right now, getting our facts together," said Trenton Police Director Irving Bradley.
The building that houses the restaurant is currently for sale, but it's unknown if that had anything to do with the deaths.
One of the victims was a friend of Trenton police spokesman Sgt. Pedro Medina.
"It's difficult. Anyone's death is difficult, especially under these circumstances. But, again, it's ongoing, the detectives are doing everything they can, they're doing a thorough investigation," Sgt. Medina said.
Police identified the victims as 44-year-old Juan Reyes and 51-year-old Jose Peralta, but released no further information.
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