Locals were startled at around 11AM local time on Thursday November 2 when a loud boom was heard followed by a gentle shaking.
Experts are still unsure as to what caused the strange phenomenon after the US Geological Survey (USGS) ruled out the possibility of it being an earthquake.
Another possible cause was that a training session at Camp Pendleton was scheduled for Thursday, but military officials said that it is unlikely residents would of heard, let alone felt, the impact of mortar fire.
One unnamed person told Fox 5 San Diego: .”I heard the boom! I live in Spring Valley thought it was construction, but I didn’t feel any shaking.
“About a week or two ago I heard the exact same boom and few seconds later my bed and walls started rocking it stopped for like two seconds and started shaking again.
“I didn’t see any reports on an earthquake that day and I asked people if they had felt it and no one did so I just ignored it.”
Another unnamed eye-witness said: “I heard it about 15 minutes ago. Not sure of the direction. But my house shook and my curtains blew inward.”
According to one expert, the boom and shaking could have a meteorological explanation.
Geologist and Weather Expert Dr Pat Abbott said: “If anything happened in the ground we would have known, because we monitor that. So, that means it’s up in the atmosphere.”
He said that it could have been a meteor entering the Earth’s atmosphere where it exploded, or cold and warm air could have clashed.
Dr Abbot: “You can get enough contrast between colder air and warmer air for example that will almost act like a reflecting board.
“So some sound can go up hit some other surface and go over an area like an unexpected area.”