Both had been shot in the head, said sheriff's homicide Lt. John Schultz. Whoever killed them also set a fire, he added.
"The suspect(s) had lit a fire in the residence that caused little damage," Schultz wrote in a statement.
"It appears the fire was set in what was an unsuccessful attempt to burn evidence," Schultz said.
He also said there were no signs of forced entry into the home.
Forensics experts collected "numerous items of evidence," to be examined for DNA and fingerprint evidence, Schultz said.
Brooklyn native Jan Pawek Pietrzak was part of the 3rd Marine Aircraft Wing at the base near Oceanside, said Marine Cpl. Michael Stevens.
He worked as a helicopter mainframe mechanic with the Marine Medium Helicopter Squadron, according to Marine Capt. Staci Reidinger.
Pietrzak enlisted in the Marines on March 7, 2003, and was promoted to sergeant at the start of this year, according to the captain.
He served in Iraq from July 2005 to February 2006.
His awards included the National Defense Service Medal, Global War on Terrorism Expeditionary Medal, Global War on Terrorism Service Medal, U.S. Marine Corps Good Conduct Medal, Sea Service Deployment Ribbon and a Certificate of Commendation and Letter of Appreciation.
The Marines could not say whether the sergeant's wife worked at the base hospital, as neighbors of the couple seemed to think.
Neighbors expressed shock and said the lack of information known about the deaths made them concerned for their own safety.
"I've lived here two years and nothing ever happened," said neighbor Mitch Tobrinen, who added that when he got home and heard about the discovery of the bodies, he was afraid to go into his own home.
Homes in the area had been selling for around $600,000, but with the economic downturn, some are now in foreclosure, for sale or for rent. Doreen Caouette, who lives on nearby Peregrine Street, said some homes in the neighborhood had recently sold for as little as $220,000.
Residents said the foreclosures have led to burglaries in the area.