Deputies said the body of Eneiga Beltan, 32, was found in the back seat of a sport utility vehicle parked in the Motel 6 parking lot Friday afternoon.
Her estranged partner, 39-year-old Hugo Gonzalez, was found in one of the rooms.
Investigators believe he shot and killed himself.
Friends and family members say the couple had recently broken up.
They have an 11-year-old son.