Newark police found the two victims deceased in a room at the E-Z 8 Motel at 5555 Cedar Court at 11:48 a.m., police said.
The two victims, the missing girl and a man from Livermore, had been shot and were pronounced dead at the scene, according to Pleasanton police.
Newark police are investigating the deaths as either a murder-suicide or a double suicide.
The girl was reported missing by her mother in Pleasanton on Sept. 10 at 9:55 p.m. Her mother did not know where her daughter might be, but suspected she may be with her boyfriend, Pleasanton police said.
Police did not confirm whether the man found dead in the room was the girl's boyfriend. The two victims' identity has not been released pending notification of their next of kin.
The motel is located near Interstate Highway 880 as well as Mowry Avenue and Cedar Boulevard.
Newark police said anyone with information about the case should contact Detective Elsa Cervantes at (510) 578-4738.
They said information can also be left anonymously on the "Silent Witness" hotline at (510) 578-4965.