Killgore had been missing since Friday, just days after she filed for divorce from her husband, Lance Cpl. Cory Killgore.
A maintenance worker clearing brush found the body on Tuesday afternoon.
Meanwhile, Jessica Lynn Lopez will be arraigned on murder charges in Killgore's death on Thursday.
Police say a suicide note written by Lopez led them to the location where Killgore's body was found. Lopez, 25, was arrested at a Ramada Inn near the San Diego International Airport. Investigators said she had to be hospitalized for a number of self-inflicted wounds in an apparent suicide attempt. Lopez's note detailed the murder and the location of the body, said authorities.
An anonymous neighbor told KGTV, Eyewitness News' sister station in San Diego, that Brittany Killgore and Lopez were involved in some kind of sex ring that they knew was dangerous.
A Marine is also in custody on an unrelated charge. Louis Ray Perez, 45, was arrested for possessing a gun stolen from Camp Pendleton. Investigators say they believe Perez was the last person to be seen with Brittany Killgore.
Cory Killgore has been on tour in Afghanistan. Friends of the couple say the two were having problems.
"She's just been doing her own thing and telling everyone for about a year that she's been planning on getting a divorce. Every time he goes away like to training or like Afghanistan, she decides that it's time to party," said neighbor Simeon Pagdilao.
As the investigation continues, Cory Killgore is now on his way back to San Diego from overseas. Police do not believe he is connected to his wife's disappearance.