Monica Thomas-Harris and Curtis "Keno" Harris, who were reported missing Thursday night, when relatives asked for the public's help in finding the 37-year-old woman who reportedly disappeared.
One employee said he knew it was them because he checked Harris' identification before renting him the $55-a-night room.
Another employee, Lawrence Parra, said he recognized the couple from photos in the newspaper.
"She was standing outside as he was getting the room," Parra said.
Police received a call about 11:20 a.m. of a person down in the motel room. When they arrived, they discovered the man and woman were dead.
"It does appear to be a murder-suicide," said public information officer Diana Salazar. "We are not looking for any outstanding suspects."
Salazar would confirm only that a black man from Chino and a black woman from Upland, both in their 30s, were found dead in Room 208 in the motel at 11435 Whittier Blvd.
Police said the man used a handgun to kill the woman before killing himself.
Neighbors said they did not hear any noises from the motel room Friday night.
"I know gunshots, and there were no gunshots," said Juan Montiel, a Petaluma resident who was staying at the motel with his wife.
The missing couple were reportedly traveling in a 2001 Ford Expedition, with the license-plate number of 4UGR263. The same vehicle was seen parked at the motel and being towed by police for evidence on Saturday.
One employee, who did not want to be identified, said he became suspicious when the couple did not check out at 11 a.m. Saturday. After repeated calls to the room, he sent a maid to check up on the couple.