Residents from Chula Vista to Oceanside reported a large rumble around 12:45 p.m. Friday.
The mysterious sensation was described by some people as sounding like a door slamming while others said it was strong enough to rattle windows.
A check of the U.S. Geological Survey website showed no earthquake activity.
Two months ago, when San Diegans heard a similar sound, there was evidence of chaff on weather radar. Chaff is a material sometimes emitted during military exercises.
On Friday, however, Tina Stall with the National Weather Service said there was no visible chaff in the area at the time the noise was reported.
The mysterious sound had both residents and experts scratching their heads. Scripps Institution of Oceanography scientist Kristoffer Walker said he felt it too, and looked into microphones recorded from MCAS Miramar.
Evidence from his research revealed an answer.
"There was indeed an atmospheric tremor, or 'skyquake,'" Walker said. "The likely cause of these 'skyquakes' is routine military activity very far off the coast of San Diego (at least 50 miles away) in zones that are designated military training zones."
Typically, we don't hear these "skyquakes." But when the wind reaches speeds of over 100 miles per hour, the sound can reach parts of San Diego, Walker said.
A spokesperson from Camp Pendleton said Marines are not training with anything unusual. They often train with various military equipment and will be training with tanks both Saturday and Sunday.
On Friday evening, the U.S. Naval Air Forces official Facebook page posted the following message regarding the mysterious boom heard around San Diego:
“San Diego, it looks like the boom that was heard and felt today was likely due to some aircraft associated with the USS Carl Vinson (CVN 70) family day cruise. As part of a flight demonstration two F/A-18 aircraft went supersonic about 35 miles off the coast. Sorry for any inconvenience this may have caused. -- LT Aaron Kakiel, media officer.”
So, according to the Navy, it appears Friday's San Diego boom mystery has finally been solved.