The San Ysidro couple - a 52-year-old man and a 45-year-old woman - was reported missing by their three children right before Christmas.
U.S. Customs and Border Patrol officers Tuesday found the married couple dead inside a vehicle parked at the Golden Acorn Casino parking lot in Campo, according to the San Diego Police Department.
Police said the man died from a self-inflicted single gunshot wound to the head. The woman's injuries remain undetermined, but her death is being investigated as a homicide.
Her husband is the lone suspect in what appears to be a "tragic case of domestic violence," police said.
The two were separated before they disappeared under suspicious circumstances last week. A domestic violence incident likely happened before they went missing, police said.
Their names have not been released until family is notified.