Officers were called to the Motel 6 at 125 Silver Leaf Drive around 2 p.m. after housecleaning staff reported finding Isabella's body.
A preliminary investigation indicated the girl died of strangulation, and her mother has been arrested and booked into Santa Cruz County Jail on suspicion of murder.
Formal charges will likely be filed this afternoon against the mother, Aptos resident Veva Virgil, 37, according to the Santa Cruz County District Attorney's Office.
Thompson said Virgil is scheduled to be arraigned Wednesday morning.
Police learned that Virgil had checked into the motel room Saturday and left Sunday morning, Thompson said.
"She left and it didn't appear she had any intention of returning," he said.
Virgil was contacted and allegedly confessed to "acting alone to kill the child in a motel room at Motel 6," Thompson said.
"She was living in Aptos with her husband and she came down and rented the room and stayed at least one night," Thompson said. "She left the next day and left the child deceased in the room."
Thompson said Virgil's husband is Isabella's stepfather.
While police initially investigated the possibility that Virgil had an accomplice in the killing, no other arrests have been made, Thompson said.
"We're currently not seeking any other involved parties," Thompson.
The murder is the city's third of the year. Two gang-related homicides were reported in October, Thompson said.